Genetic loci associated with soybean cyst nematode resistance and methods of use

ABSTRACT

Various methods and compositions are provided for identifying and/or selecting soybean plants or soybean germplasm with resistance or improved resistance to soybean cyst nematode. In certain embodiments, the method comprises detecting at least one marker locus that is associated with resistance to soybean cyst nematode. In other embodiments, the method further comprises detecting at least one marker profile or haplotype associated with resistance to soybean cyst nematode. In further embodiments, the method comprises crossing a selected soybean plant with a second soybean plant. Further provided are markers, primers, probes and kits useful for identifying and/or selecting soybean plants or soybean germplasm with resistance or improved resistance to soybean cyst nematode.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application No.61/740,567, filed Dec. 21, 2012, which is hereby incorporated herein inits entirety by reference.

FIELD OF THE INVENTION

This invention relates to methods of identifying and/or selectingsoybean plants or germplasm that display resistance or improvedresistance to Soybean Cyst Nematode.

REFERENCE TO A SEQUENCE LISTING SUBMITTED AS A TEXT FILE VIA EFS-WEB

The official copy of the sequence listing is submitted concurrently withthe specification as a text file via EFS-Web, in compliance with theAmerican Standard Code for Information Interchange (ASCII), with a filename of 430267seqlist.txt, a creation date of Feb. 21, 2013 and a sizeof 229 KB. The sequence listing filed via EFS-Web is part of thespecification and is hereby incorporated in its entirety by referenceherein.

BACKGROUND

Soybeans (Glycine max L. Merr.) are a major cash crop and investmentcommodity in North America and elsewhere. Soybean oil is one of the mostwidely used edible oils, and soybeans are used worldwide both in animalfeed and in human food production. Additionally, soybean utilization isexpanding to industrial, manufacturing, and pharmaceutical applications.

Soybean Cyst Nematode (SCN) is a parasitic pest which has threatenedsoybean production in the U.S. for more than fifty years. Soybean cystnematode resistance is an economically important trait as infection cansubstantially reduce yields. Molecular characterization of soybean cystnematode resistance would have important implications for soybeancultivar improvement.

There remains a need for soybean plants with improved resistance tosoybean cyst nematode and methods for identifying and selecting suchplants.

SUMMARY

Various methods and compositions are provided for identifying and/orselecting soybean plants or soybean germplasm with resistance orimproved resistance to soybean cyst nematode. In certain embodiments,the method comprises detecting at least one marker locus that isassociated with resistance to soybean cyst nematode. In otherembodiments, the method further comprises detecting at least one markerprofile or haplotype associated with resistance to soybean cystnematode. In further embodiments, the method comprises crossing aselected soybean plant with a second soybean plant. Further provided aremarkers, primers, probes and kits useful for identifying and/orselecting soybean plants or soybean germplasm with resistance orimproved resistance to soybean cyst nematode.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 A-D provides a genetic map for loci on linkage group A2.

DETAILED DESCRIPTION

Before describing the present invention in detail, it is to beunderstood that this invention is not limited to particular embodiments,which can, of course, vary. It is also to be understood that theterminology used herein is for the purpose of describing particularembodiments only, and is not intended to be limiting.

Certain definitions used in the specification and claims are providedbelow. In order to provide a clear and consistent understanding of thespecification and claims, including the scope to be given such terms,the following definitions are provided:

As used in this specification and the appended claims, terms in thesingular and the singular forms “a,” “an,” and “the,” for example,include plural referents unless the content clearly dictates otherwise.Thus, for example, reference to “plant,” “the plant,” or “a plant” alsoincludes a plurality of plants; also, depending on the context, use ofthe term “plant” can also include genetically similar or identicalprogeny of that plant; use of the term “a nucleic acid” optionallyincludes, as a practical matter, many copies of that nucleic acidmolecule; similarly, the term “probe” optionally (and typically)encompasses many similar or identical probe molecules.

Additionally, as used herein, “comprising” is to be interpreted asspecifying the presence of the stated features, integers, steps, orcomponents as referred to, but does not preclude the presence oraddition of one or more features, integers, steps, or components, orgroups thereof. Thus, for example, a kit comprising one pair ofoligonucleotide primers may have two or more pairs of oligonucleotideprimers. Additionally, the term “comprising” is intended to includeexamples encompassed by the terms “consisting essentially of” and“consisting of.” Similarly, the term “consisting essentially of” isintended to include examples encompassed by the term “consisting of.”

“Agronomics,” “agronomic traits,” and “agronomic performance” refer tothe traits (and underlying genetic elements) of a given plant varietythat contribute to yield over the course of a growing season. Individualagronomic traits include emergence vigor, vegetative vigor, stresstolerance, disease resistance or tolerance, insect resistance ortolerance, herbicide resistance, branching, flowering, seed set, seedsize, seed density, standability, threshability, and the like.

“Allele” means any of one or more alternative forms of a geneticsequence. In a diploid cell or organism, the two alleles of a givensequence typically occupy corresponding loci on a pair of homologouschromosomes. With regard to a SNP marker, allele refers to the specificnucleotide base present at that SNP locus in that individual plant.

The term “amplifying” in the context of nucleic acid amplification isany process whereby additional copies of a selected nucleic acid (or atranscribed form thereof) are produced. An “amplicon” is an amplifiednucleic acid, e.g., a nucleic acid that is produced by amplifying atemplate nucleic acid by any available amplification method.

An “ancestral line” is a parent line used as a source of genes, e.g.,for the development of elite lines.

An “ancestral population” is a group of ancestors that have contributedthe bulk of the genetic variation that was used to develop elite lines.

“Backcrossing” is a process in which a breeder crosses a progeny varietyback to one of the parental genotypes one or more times.

The term “chromosome segment” designates a contiguous linear span ofgenomic DNA that resides in planta on a single chromosome. “Chromosomeinterval” refers to a chromosome segment defined by specific flankingmarker loci.

“Cultivar” and “variety” are used synonymously and mean a group ofplants within a species (e.g., Glycine max) that share certain genetictraits that separate them from other possible varieties within thatspecies. Soybean cultivars are inbred lines produced after severalgenerations of self-pollinations. Individuals within a soybean cultivarare homogeneous, nearly genetically identical, with most loci in thehomozygous state.

An “elite line” is an agronomically superior line that has resulted frommany cycles of breeding and selection for superior agronomicperformance. Numerous elite lines are available and known to those ofskill in the art of soybean breeding.

An “elite population” is an assortment of elite individuals or linesthat can be used to represent the state of the art in terms ofagronomically superior genotypes of a given crop species, such assoybean.

An “exotic soybean strain” or an “exotic soybean germplasm” is a strainor germplasm derived from a soybean not belonging to an available elitesoybean line or strain of germplasm. In the context of a cross betweentwo soybean plants or strains of germplasm, an exotic germplasm is notclosely related by descent to the elite germplasm with which it iscrossed. Most commonly, the exotic germplasm is not derived from anyknown elite line of soybean, but rather is selected to introduce novelgenetic elements (typically novel alleles) into a breeding program.

A “genetic map” is a description of genetic association or linkagerelationships among loci on one or more chromosomes (or linkage groups)within a given species, generally depicted in a diagrammatic or tabularform.

“Genotype” is a description of the allelic state at one or more loci.

“Germplasm” means the genetic material that comprises the physicalfoundation of the hereditary qualities of an organism. As used herein,germplasm includes seeds and living tissue from which new plants may begrown; or, another plant part, such as leaf, stem, pollen, or cells,that may be cultured into a whole plant. Germplasm resources providesources of genetic traits used by plant breeders to improve commercialcultivars.

An individual is “homozygous” if the individual has only one type ofallele at a given locus (e.g., a diploid individual has a copy of thesame allele at a locus for each of two homologous chromosomes). Anindividual is “heterozygous” if more than one allele type is present ata given locus (e.g., a diploid individual with one copy each of twodifferent alleles). The term “homogeneity” indicates that members of agroup have the same genotype at one or more specific loci. In contrast,the term “heterogeneity” is used to indicate that individuals within thegroup differ in genotype at one or more specific loci.

“Introgression” means the entry or introduction of a gene, QTL,haplotype, marker profile, trait, or trait locus from the genome of oneplant into the genome of another plant.

The terms “label” or “detectable label” refer to a molecule capable ofdetection. A detectable label can also include a combination of areporter and a quencher, such as are employed in FRET probes or TaqMan™probes. The term “reporter” refers to a substance or a portion thereofwhich is capable of exhibiting a detectable signal, which signal can besuppressed by a quencher. The detectable signal of the reporter is,e.g., fluorescence in the detectable range. The term “quencher” refersto a substance or portion thereof which is capable of suppressing,reducing, inhibiting, etc., the detectable signal produced by thereporter. As used herein, the terms “quenching” and “fluorescence energytransfer” refer to the process whereby, when a reporter and a quencherare in close proximity, and the reporter is excited by an energy source,a substantial portion of the energy of the excited state non-radiativelytransfers to the quencher where it either dissipates non-radiatively oris emitted at a different emission wavelength than that of the reporter.

A “line” or “strain” is a group of individuals of identical parentagethat are generally inbred to some degree and that are generallyhomozygous and homogeneous at most loci (isogenic or near isogenic). A“subline” refers to an inbred subset of descendants that are geneticallydistinct from other similarly inbred subsets descended from the sameprogenitor. Traditionally, a subline has been derived by inbreeding theseed from an individual soybean plant selected at the F3 to F5generation until the residual segregating loci are “fixed” or homozygousacross most or all loci. Commercial soybean varieties (or lines) aretypically produced by aggregating (“bulking”) the self-pollinatedprogeny of a single F3 to F5 plant from a controlled cross between 2genetically different parents. While the variety typically appearsuniform, the self-pollinating variety derived from the selected planteventually (e.g., F8) becomes a mixture of homozygous plants that canvary in genotype at any locus that was heterozygous in the originallyselected F3 to F5 plant. Marker-based sublines that differ from eachother based on qualitative polymorphism at the DNA level at one or morespecific marker loci are derived by genotyping a sample of seed derivedfrom individual self-pollinated progeny derived from a selected F3-F5plant. The seed sample can be genotyped directly as seed, or as planttissue grown from such a seed sample. Optionally, seed sharing a commongenotype at the specified locus (or loci) are bulked providing a sublinethat is genetically homogenous at identified loci important for a traitof interest (e.g., yield, tolerance, etc.).

“Linkage” refers to the tendency for alleles to segregate together moreoften than expected by chance if their transmission was independent.Typically, linkage refers to alleles on the same chromosome. Geneticrecombination occurs with an assumed random frequency over the entiregenome. Genetic maps are constructed by measuring the frequency ofrecombination between pairs of traits or markers, the lower thefrequency of recombination, and the greater the degree of linkage.“Linkage disequilibrium” is a non-random association of alleles at twoor more loci and can occur between unlinked markers. It is based onallele frequencies within a population and is influenced by but notdependent on linkage.

“Linkage group” (LG) refers to traits or markers that generallyco-segregate. A linkage group generally corresponds to a chromosomalregion containing genetic material that encodes the traits or markers.

“Locus” is a defined segment of DNA.

A “map location” or “map position” is an assigned location on a geneticmap relative to linked genetic markers where a specified marker can befound within a given species. Map positions are generally provided incentimorgans (cM), unless otherwise indicated, genetic positionsprovided are based on the Glycine max consensus map v 4.0 as provided byHyten et al. (2010) Crop Sci 50:960-968. A “physical position” or“physical location” or “physical map location” is the position,typically in nucleotides bases, of a particular nucleotide, such as aSNP nucleotide, on a chromosome. Unless otherwise indicated, thephysical position within the soybean genome provided is based on theGlyma 1.0 genome sequence described in Schmutz et al. (2010) Nature463:178-183, available from the Phytozome website(phytozome-dot-net/soybean).

“Mapping” is the process of defining the association and relationshipsof loci through the use of genetic markers, populations segregating forthe markers, and standard genetic principles of recombination frequency.

“Marker” or “molecular marker” or “marker locus” is a term used todenote a nucleic acid or amino acid sequence that is sufficiently uniqueto characterize a specific locus on the genome. Any detectablepolymorphic trait can be used as a marker so long as it is inheriteddifferentially and exhibits linkage disequilibrium with a phenotypictrait of interest.

“Marker assisted selection” refers to the process of selecting a desiredtrait or traits in a plant or plants by detecting one or more nucleicacids from the plant, where the nucleic acid is linked to the desiredtrait, and then selecting the plant or germplasm possessing those one ormore nucleic acids.

“Haplotype” refers to a combination of particular alleles present withina particular plant's genome at two or more linked marker loci, forinstance at two or more loci on a particular linkage group. Forinstance, in one example, two specific marker loci on LG-A2 are used todefine a haplotype for a particular plant. In still further examples, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or morelinked marker loci are used to define a haplotype for a particularplant.

As used herein, a “marker profile” means a combination of particularalleles present within a particular plant's genome at two or more markerloci which are not linked, for instance two or more loci on two or moredifferent linkage groups or two or more chromosomes. For instance, inone example, a particular combination of marker loci or a particularcombination of haplotypes define the marker profile of a particularplant.

The term “plant” includes reference to an immature or mature wholeplant, including a plant from which seed or grain or anthers have beenremoved. Seed or embryo that will produce the plant is also consideredto be the plant.

“Plant parts” means any portion or piece of a plant, including leaves,stems, buds, roots, root tips, anthers, seed, grain, embryo, pollen,ovules, flowers, cotyledons, hypocotyls, pods, flowers, shoots, stalks,tissues, tissue cultures, cells and the like.

“Polymorphism” means a change or difference between two related nucleicacids. A “nucleotide polymorphism” refers to a nucleotide that isdifferent in one sequence when compared to a related sequence when thetwo nucleic acids are aligned for maximal correspondence.

“Polynucleotide,” “polynucleotide sequence,” “nucleic acid,” “nucleicacid molecule,” “nucleic acid sequence,” “nucleic acid fragment,” and“oligonucleotide” are used interchangeably herein to indicate a polymerof nucleotides that is single- or multi-stranded, that optionallycontains synthetic, non-natural, or altered RNA or DNA nucleotide bases.A DNA polynucleotide may be comprised of one or more strands of cDNA,genomic DNA, synthetic DNA, or mixtures thereof.

“Primer” refers to an oligonucleotide which is capable of acting as apoint of initiation of nucleic acid synthesis or replication along acomplementary strand when placed under conditions in which synthesis ofa complementary strand is catalyzed by a polymerase. Typically, primersare about 10 to 30 nucleotides in length, but longer or shortersequences can be employed. Primers may be provided in double-strandedform, though the single-stranded form is more typically used. A primercan further contain a detectable label, for example a 5′ end label.

“Probe” refers to an oligonucleotide that is complementary (though notnecessarily fully complementary) to a polynucleotide of interest andforms a duplexed structure by hybridization with at least one strand ofthe polynucleotide of interest. Typically, probes are oligonucleotidesfrom 10 to 50 nucleotides in length, but longer or shorter sequences canbe employed. A probe can further contain a detectable label.

“Quantitative trait loci” or “QTL” refer to the genetic elementscontrolling a quantitative trait.

“Recombination frequency” is the frequency of a crossing over event(recombination) between two genetic loci. Recombination frequency can beobserved by following the segregation of markers and/or traits duringmeiosis.

“Resistance and “improved resistance” are used interchangeably hereinand refer to any type of increase in resistance or tolerance to, or anytype of decrease in susceptibility. A “resistant plant” or “resistantplant variety” need not possess absolute or complete resistance.Instead, a “resistant plant,” “resistant plant variety,” or a plant orplant variety with “improved resistance” will have a level of resistanceor tolerance which is higher than that of a comparable susceptible plantor variety.

“Self-crossing” or “self-pollination” or “selfing” is a process throughwhich a breeder crosses a plant with itself; for example, a secondgeneration hybrid F2 with itself to yield progeny designated F2:3.

“SNP” or “single nucleotide polymorphism” means a sequence variationthat occurs when a single nucleotide (A, T, C, or G) in the genomesequence is altered or variable. “SNP markers” exist when SNPs aremapped to sites on the soybean genome.

The term “yield” refers to the productivity per unit area of aparticular plant product of commercial value. For example, yield ofsoybean is commonly measured in bushels of seed per acre or metric tonsof seed per hectare per season. Yield is affected by both genetic andenvironmental factors.

As used herein, an “isolated” or “purified” polynucleotide orpolypeptide, or biologically active portion thereof, is substantially oressentially free from components that normally accompany or interactwith the polynucleotide or polypeptide as found in its naturallyoccurring environment. Typically, an “isolated” polynucleotide is freeof sequences (optimally protein encoding sequences) that naturally flankthe polynucleotide (i.e., sequences located at the 5′ and 3′ ends of thepolynucleotide) in the genomic DNA of the organism from which thepolynucleotide is derived. For example, the isolated polynucleotide cancontain less than about 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb, or 0.1 kbof nucleotide sequence that naturally flank the polynucleotide ingenomic DNA of the cell from which the polynucleotide is derived. Apolypeptide that is substantially free of cellular material includespreparations of polypeptides having less than about 30%, 20%, 10%, 5%,or 1% (by dry weight) of contaminating protein, culture media or otherchemical components.

Standard recombinant DNA and molecular cloning techniques used hereinare well known in the art and are described more fully in Sambrook, J.,Fritsch, E. F. and Maniatis, T. Molecular Cloning: A Laboratory Manual;Cold Spring Harbor Laboratory Press: Cold Spring Harbor, 1989(hereinafter “Sambrook”).

Methods are provided for identifying and/or selecting a soybean plant orsoybean germplasm that displays resistance or improved resistance tosoybean cyst nematode. The method comprises detecting in the soybeanplant or germplasm, or a part thereof, at least one marker locusassociated with resistance to soybean cyst nematode. Also provided areisolated polynucleotides and kits for use in identifying and/ordetecting a soybean plant or soybean germplasm that displays resistanceor improved resistance to soybean cyst nematode, and soybean plants,cells, and/or seeds comprising at least one marker locus conferringimproved resistance to soybean cyst nematode.

Provided herein, marker loci associated with soybean cyst nematoderesistance have been identified and mapped to the rhg4 (resistance toHeterodera glycines 4) locus on linkage group A2 on chromosome 8.Examples of soybean lines known to comprise the rhg4 resistance locusinclude, for example, Peking and PI437654.

These findings have important implications for soybean production, asidentifying markers that can be used for selection of soybean cystnematode resistance will greatly expedite the development of soybeancyst nematode resistance into elite cultivars.

Marker loci, haplotypes and marker profiles associated with resistanceto soybean cyst nematode, are provided. Further provided are genomicloci that are associated with soybean resistance to soybean cystnematode.

In certain embodiments, soybean plants or germplasm are identified thathave at least one favorable allele, marker locus, haplotype or markerprofile that positively correlates with resistance or improvedresistance to soybean cyst nematode. However, in other embodiments, itis useful for exclusionary purposes during breeding to identify alleles,marker loci, haplotypes, or marker profiles that negatively correlatewith resistance, for example, to eliminate such plants or germplasm fromsubsequent rounds of breeding.

In one embodiment, marker loci useful for identifying a first soybeanplant or first soybean germplasm that displays resistance or improvedresistance to soybean cyst nematode are associated with the rhg4 locuson linkage group A2 on chromosome 8. In another embodiment, the markerlocus comprises: (a) S07160-1 or a closely linked marker on linkagegroup A2; or (b) Gm08:8300131, Gm08:8257778, Gm08:8257785, Gm08:8258163,Gm08:8258688, Gm08:8258742, Gm08:8259928, Gm08:8260451, Gm08:8260590,Gm08:8261480, Gm08:8261684, Gm08:8262165, Gm08:8263213, Gm08:8263250,Gm08:8263611, Gm08:8264149, Gm08:8265227, Gm08:8265364, Gm08:8265614,Gm08:8266183, Gm08:8266185, Gm08:8266263, Gm08:8266350, Gm08:8266386,Gm08:8266473, Gm08:8266888, Gm08:8267085, Gm08:8267166, Gm08:8267721,Gm08:8267826, Gm08:8268336, Gm08:8268861, Gm08:8269148, Gm08:8269785,Gm08:8270037, Gm08:8270562, Gm08:8270652, Gm08:8271540, Gm08:8271591,Gm08:8271649, Gm08:8271672, Gm08:8271955, Gm08:8273257, Gm08:8273355,Gm08:8273979, Gm08:8275766, Gm08:8275780, Gm08:8275959, Gm08:8276701,Gm08:8276849, Gm08:8276913, Gm08:8277162, Gm08:8277227, Gm08:8277248,Gm08:8277381, Gm08:8277383, Gm08:8277542, Gm08:8277625, Gm08:8277643,Gm08:8277876, Gm08:8277880, Gm08:8277969, Gm08:8278001, Gm08:8278167,Gm08:8278274, Gm08:8278434, Gm08:8279165, Gm08:8279230, Gm08:8279854,Gm08:8280901, Gm08:8280937, Gm08:8281564, Gm08:8282902, Gm08:8284027,Gm08:8286864, Gm08:8287265, Gm08:8287278, Gm08:8287453, Gm08:8287459,Gm08:8288039, Gm08:8288141, Gm08:8288200, Gm08:8288470, Gm08:8288831,Gm08:8289392, Gm08:8290740, Gm08:8291682, Gm08:8292207, Gm08:8297064,Gm08:8299433, Gm08:8299672, Gm08:8301839, Gm08:8302134, Gm08:8303450,Gm08:8305237, Gm08:8305348, Gm08:8305905, Gm08:8306090, Gm08:8306141,Gm08:8306210, Gm08:8306492, Gm08:8306627, Gm08:8307172, Gm08:8307665,Gm08:8308019, Gm08:8308891, Gm08:8308917, Gm08:8309316, Gm08:8309423,Gm08:8309837, Gm08:8310383, Gm08:8310464, Gm08:8310503, Gm08:8310663,Gm08:8311631, Gm08:8311906, Gm08:8312536, Gm08:8312819, Gm08:8313273,Gm08:8313923, Gm08:8314010, Gm08:8314025, Gm08:8314208, Gm08:8314292,Gm08:8314295, Gm08:8314513, Gm08:8314736, Gm08:8314791, Gm08:8314860,Gm08:8315543, Gm08:8315644, Gm08:8316113, Gm08:8316689, Gm08:8316899,Gm08:8317852, Gm08:8317861, Gm08:8318033, Gm08:8319087, Gm08:8319642,Gm08:8319647, Gm08:8320068, Gm08:8321253, Gm08:8321649, Gm08:8323937,Gm08:8324341, Gm08:8325127, Gm08:8325214, Gm08:8326696, Gm08:8326877,Gm08:8328633, Gm08:8330929, Gm08:8331132, Gm08:8331181, Gm08:8331408,Gm08:8331827, Gm08:8332651, Gm08:8332685, Gm08:8332957, Gm08:8343167,Gm08:8345187, Gm08:8345720, Gm08:8346030, Gm08:8346050, Gm08:8346352,Gm08:8346726, Gm08:8347799, Gm08:8348022, Gm08:8348028, Gm08:8349925,Gm08:8350122, Gm08:8350277, Gm08:8351061, Gm08:8351503, Gm08:8352313,Gm08:8352743, Gm08:8353341, Gm08:8355175, Gm08:8360133, Gm08:8363193,Gm08:8363888, Gm08:8364195 or a marker closely linked thereto.

In certain embodiments, multiple marker loci that collectively make up asoybean cyst nematode resistance haplotype of interest are investigated.For example, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more of the various markerloci provided herein can comprise a soybean cyst nematode resistancehaplotype. In some embodiments, the haplotype comprises: (a) two or moremarker loci associated with the Rhg4 locus on linkage group A2; or (b)two or more marker loci comprising S07160-1, Gm08:8300131, Gm08:8257778,Gm08:8257785, Gm08:8258163, Gm08:8258688, Gm08:8258742, Gm08:8259928,Gm08:8260451, Gm08:8260590, Gm08:8261480, Gm08:8261684, Gm08:8262165,Gm08:8263213, Gm08:8263250, Gm08:8263611, Gm08:8264149, Gm08:8265227,Gm08:8265364, Gm08:8265614, Gm08:8266183, Gm08:8266185, Gm08:8266263,Gm08:8266350, Gm08:8266386, Gm08:8266473, Gm08:8266888, Gm08:8267085,Gm08:8267166, Gm08:8267721, Gm08:8267826, Gm08:8268336, Gm08:8268861,Gm08:8269148, Gm08:8269785, Gm08:8270037, Gm08:8270562, Gm08:8270652,Gm08:8271540, Gm08:8271591, Gm08:8271649, Gm08:8271672, Gm08:8271955,Gm08:8273257, Gm08:8273355, Gm08:8273979, Gm08:8275766, Gm08:8275780,Gm08:8275959, Gm08:8276701, Gm08:8276849, Gm08:8276913, Gm08:8277162,Gm08:8277227, Gm08:8277248, Gm08:8277381, Gm08:8277383, Gm08:8277542,Gm08:8277625, Gm08:8277643, Gm08:8277876, Gm08:8277880, Gm08:8277969,Gm08:8278001, Gm08:8278167, Gm08:8278274, Gm08:8278434, Gm08:8279165,Gm08:8279230, Gm08:8279854, Gm08:8280901, Gm08:8280937, Gm08:8281564,Gm08:8282902, Gm08:8284027, Gm08:8286864, Gm08:8287265, Gm08:8287278,Gm08:8287453, Gm08:8287459, Gm08:8288039, Gm08:8288141, Gm08:8288200,Gm08:8288470, Gm08:8288831, Gm08:8289392, Gm08:8290740, Gm08:8291682,Gm08:8292207, Gm08:8297064, Gm08:8299433, Gm08:8299672, Gm08:8301839,Gm08:8302134, Gm08:8303450, Gm08:8305237, Gm08:8305348, Gm08:8305905,Gm08:8306090, Gm08:8306141, Gm08:8306210, Gm08:8306492, Gm08:8306627,Gm08:8307172, Gm08:8307665, Gm08:8308019, Gm08:8308891, Gm08:8308917,Gm08:8309316, Gm08:8309423, Gm08:8309837, Gm08:8310383, Gm08:8310464,Gm08:8310503, Gm08:8310663, Gm08:8311631, Gm08:8311906, Gm08:8312536,Gm08:8312819, Gm08:8313273, Gm08:8313923, Gm08:8314010, Gm08:8314025,Gm08:8314208, Gm08:8314292, Gm08:8314295, Gm08:8314513, Gm08:8314736,Gm08:8314791, Gm08:8314860, Gm08:8315543, Gm08:8315644, Gm08:8316113,Gm08:8316689, Gm08:8316899, Gm08:8317852, Gm08:8317861, Gm08:8318033,Gm08:8319087, Gm08:8319642, Gm08:8319647, Gm08:8320068, Gm08:8321253,Gm08:8321649, Gm08:8323937, Gm08:8324341, Gm08:8325127, Gm08:8325214,Gm08:8326696, Gm08:8326877, Gm08:8328633, Gm08:8330929, Gm08:8331132,Gm08:8331181, Gm08:8331408, Gm08:8331827, Gm08:8332651, Gm08:8332685,Gm08:8332957, Gm08:8343167, Gm08:8345187, Gm08:8345720, Gm08:8346030,Gm08:8346050, Gm08:8346352, Gm08:8346726, Gm08:8347799, Gm08:8348022,Gm08:8348028, Gm08:8349925, Gm08:8350122, Gm08:8350277, Gm08:8351061,Gm08:8351503, Gm08:8352313, Gm08:8352743, Gm08:8353341, Gm08:8355175,Gm08:8360133, Gm08:8363193, Gm08:8363888, Gm08:8364195 or a markerclosely linked thereto.

In one embodiment, the method of identifying a first soybean plant or afirst soybean germplasm that displays resistance or improved resistanceto soybean cyst nematode comprises detecting in the genome of the firstsoybean plant or in the genome of the first soybean germplasm at leastone haplotype that is associated with the resistance, wherein the atleast one haplotype comprises at least two of the various marker lociprovided herein.

In certain embodiments, two or more marker loci or haplotypes cancollectively make up a marker profile. The marker profile can compriseany two or more marker loci comprising: (a) marker loci comprisingS07160-1 on linkage group A2, or a closely linked marker; (b) markerloci comprising Gm08:8300131, Gm08:8257778, Gm08:8257785, Gm08:8258163,Gm08:8258688, Gm08:8258742, Gm08:8259928, Gm08:8260451, Gm08:8260590,Gm08:8261480, Gm08:8261684, Gm08:8262165, Gm08:8263213, Gm08:8263250,Gm08:8263611, Gm08:8264149, Gm08:8265227, Gm08:8265364, Gm08:8265614,Gm08:8266183, Gm08:8266185, Gm08:8266263, Gm08:8266350, Gm08:8266386,Gm08:8266473, Gm08:8266888, Gm08:8267085, Gm08:8267166, Gm08:8267721,Gm08:8267826, Gm08:8268336, Gm08:8268861, Gm08:8269148, Gm08:8269785,Gm08:8270037, Gm08:8270562, Gm08:8270652, Gm08:8271540, Gm08:8271591,Gm08:8271649, Gm08:8271672, Gm08:8271955, Gm08:8273257, Gm08:8273355,Gm08:8273979, Gm08:8275766, Gm08:8275780, Gm08:8275959, Gm08:8276701,Gm08:8276849, Gm08:8276913, Gm08:8277162, Gm08:8277227, Gm08:8277248,Gm08:8277381, Gm08:8277383, Gm08:8277542, Gm08:8277625, Gm08:8277643,Gm08:8277876, Gm08:8277880, Gm08:8277969, Gm08:8278001, Gm08:8278167,Gm08:8278274, Gm08:8278434, Gm08:8279165, Gm08:8279230, Gm08:8279854,Gm08:8280901, Gm08:8280937, Gm08:8281564, Gm08:8282902, Gm08:8284027,Gm08:8286864, Gm08:8287265, Gm08:8287278, Gm08:8287453, Gm08:8287459,Gm08:8288039, Gm08:8288141, Gm08:8288200, Gm08:8288470, Gm08:8288831,Gm08:8289392, Gm08:8290740, Gm08:8291682, Gm08:8292207, Gm08:8297064,Gm08:8299433, Gm08:8299672, Gm08:8301839, Gm08:8302134, Gm08:8303450,Gm08:8305237, Gm08:8305348, Gm08:8305905, Gm08:8306090, Gm08:8306141,Gm08:8306210, Gm08:8306492, Gm08:8306627, Gm08:8307172, Gm08:8307665,Gm08:8308019, Gm08:8308891, Gm08:8308917, Gm08:8309316, Gm08:8309423,Gm08:8309837, Gm08:8310383, Gm08:8310464, Gm08:8310503, Gm08:8310663,Gm08:8311631, Gm08:8311906, Gm08:8312536, Gm08:8312819, Gm08:8313273,Gm08:8313923, Gm08:8314010, Gm08:8314025, Gm08:8314208, Gm08:8314292,Gm08:8314295, Gm08:8314513, Gm08:8314736, Gm08:8314791, Gm08:8314860,Gm08:8315543, Gm08:8315644, Gm08:8316113, Gm08:8316689, Gm08:8316899,Gm08:8317852, Gm08:8317861, Gm08:8318033, Gm08:8319087, Gm08:8319642,Gm08:8319647, Gm08:8320068, Gm08:8321253, Gm08:8321649, Gm08:8323937,Gm08:8324341, Gm08:8325127, Gm08:8325214, Gm08:8326696, Gm08:8326877,Gm08:8328633, Gm08:8330929, Gm08:8331132, Gm08:8331181, Gm08:8331408,Gm08:8331827, Gm08:8332651, Gm08:8332685, Gm08:8332957, Gm08:8343167,Gm08:8345187, Gm08:8345720, Gm08:8346030, Gm08:8346050, Gm08:8346352,Gm08:8346726, Gm08:8347799, Gm08:8348022, Gm08:8348028, Gm08:8349925,Gm08:8350122, Gm08:8350277, Gm08:8351061, Gm08:8351503, Gm08:8352313,Gm08:8352743, Gm08:8353341, Gm08:8355175, Gm08:8360133, Gm08:8363193,Gm08:8363888, Gm08:8364195 or a marker closely linked thereto; (c) anymarker loci associated with the rhg4 locus on linkage group A2; (d) anymarker loci associated with the rhg1 locus on linkage group G, or aclosely linked marker; (e) any marker loci associated with the rhg2locus on linkage group M; and/or (f) any marker loci associated withresistance to soybean cyst nematode.

Any of the marker loci in any of the genomic loci disclosed herein canbe combined in the marker profile. For example, the marker profile cancomprise 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,20, or more marker loci or haplotypes associated with resistance tosoybean cyst nematode.

In one embodiment, a method of identifying a first soybean plant or afirst soybean germplasm that displays resistance or improved resistanceto soybean cyst nematode comprises detecting in the genome of the firstsoybean plant or in the genome of the first soybean germplasm at leastone marker profile that is associated with the resistance, wherein theat least one marker profile comprises the marker locus provided herein.

Not only can one detect the various markers provided herein, it isrecognized that one could detect any markers that are closely linked tothe various markers discussed herein. Non-limiting examples of closelylinked markers on linkage group A2 are provided in FIG. 1 A-D.

In addition to the markers discussed herein, information regardinguseful soybean markers can be found, for example, on the USDA's Soybasewebsite, available at www.soybase.org. One of skill in the art willrecognize that the identification of favorable marker alleles may begermplasm-specific. The determination of which marker alleles correlatewith resistance (or susceptibility) is determined for the particulargermplasm under study. One of skill will also recognize that methods foridentifying the favorable alleles are routine and well known in the art,and furthermore, that the identification and use of such favorablealleles is well within the scope of the invention.

Various methods are provided to identify soybean plants and/or germplasmwith resistance or improved resistance to soybean cyst nematode. In oneembodiment, the method of identifying comprises detecting at least onemarker locus associated with resistance to soybean cyst nematode. Theterm “associated with” in connection with a relationship between amarker locus and a phenotype refers to a statistically significantdependence of marker frequency with respect to a quantitative scale orqualitative gradation of the phenotype. Thus, an allele of a marker isassociated with a trait of interest when the allele of the marker locusand the trait phenotypes are found together in the progeny of anorganism more often than if the marker genotypes and trait phenotypessegregated separately.

Any combination of the marker loci provided herein can be used in themethods to identify a soybean plant or soybean germplasm that displaysresistance or improved resistance to soybean cyst nematode. Any onemarker locus or any combination of the markers set forth herein, or anyclosely linked marker can be used to aid in identifying and selectingsoybean plants or soybean germplasm with resistance or improvedresistance to soybean cyst nematode.

In one embodiment, a method of identifying a first soybean plant or afirst soybean germplasm that displays resistance or improved resistanceto soybean cyst nematode is provided. The method comprises detecting inthe genome of the first soybean plant or first soybean germplasm atleast one marker locus that is associated with resistance. In such amethod, the at least one marker locus: (a) can comprise the marker locusS07160-1 on linkage group A2, or a closely linked marker; (b) cancomprise the marker loci Gm08:8300131, Gm08:8257778, Gm08:8257785,Gm08:8258163, Gm08:8258688, Gm08:8258742, Gm08:8259928, Gm08:8260451,Gm08:8260590, Gm08:8261480, Gm08:8261684, Gm08:8262165, Gm08:8263213,Gm08:8263250, Gm08:8263611, Gm08:8264149, Gm08:8265227, Gm08:8265364,Gm08:8265614, Gm08:8266183, Gm08:8266185, Gm08:8266263, Gm08:8266350,Gm08:8266386, Gm08:8266473, Gm08:8266888, Gm08:8267085, Gm08:8267166,Gm08:8267721, Gm08:8267826, Gm08:8268336, Gm08:8268861, Gm08:8269148,Gm08:8269785, Gm08:8270037, Gm08:8270562, Gm08:8270652, Gm08:8271540,Gm08:8271591, Gm08:8271649, Gm08:8271672, Gm08:8271955, Gm08:8273257,Gm08:8273355, Gm08:8273979, Gm08:8275766, Gm08:8275780, Gm08:8275959,Gm08:8276701, Gm08:8276849, Gm08:8276913, Gm08:8277162, Gm08:8277227,Gm08:8277248, Gm08:8277381, Gm08:8277383, Gm08:8277542, Gm08:8277625,Gm08:8277643, Gm08:8277876, Gm08:8277880, Gm08:8277969, Gm08:8278001,Gm08:8278167, Gm08:8278274, Gm08:8278434, Gm08:8279165, Gm08:8279230,Gm08:8279854, Gm08:8280901, Gm08:8280937, Gm08:8281564, Gm08:8282902,Gm08:8284027, Gm08:8286864, Gm08:8287265, Gm08:8287278, Gm08:8287453,Gm08:8287459, Gm08:8288039, Gm08:8288141, Gm08:8288200, Gm08:8288470,Gm08:8288831, Gm08:8289392, Gm08:8290740, Gm08:8291682, Gm08:8292207,Gm08:8297064, Gm08:8299433, Gm08:8299672, Gm08:8301839, Gm08:8302134,Gm08:8303450, Gm08:8305237, Gm08:8305348, Gm08:8305905, Gm08:8306090,Gm08:8306141, Gm08:8306210, Gm08:8306492, Gm08:8306627, Gm08:8307172,Gm08:8307665, Gm08:8308019, Gm08:8308891, Gm08:8308917, Gm08:8309316,Gm08:8309423, Gm08:8309837, Gm08:8310383, Gm08:8310464, Gm08:8310503,Gm08:8310663, Gm08:8311631, Gm08:8311906, Gm08:8312536, Gm08:8312819,Gm08:8313273, Gm08:8313923, Gm08:8314010, Gm08:8314025, Gm08:8314208,Gm08:8314292, Gm08:8314295, Gm08:8314513, Gm08:8314736, Gm08:8314791,Gm08:8314860, Gm08:8315543, Gm08:8315644, Gm08:8316113, Gm08:8316689,Gm08:8316899, Gm08:8317852, Gm08:8317861, Gm08:8318033, Gm08:8319087,Gm08:8319642, Gm08:8319647, Gm08:8320068, Gm08:8321253, Gm08:8321649,Gm08:8323937, Gm08:8324341, Gm08:8325127, Gm08:8325214, Gm08:8326696,Gm08:8326877, Gm08:8328633, Gm08:8330929, Gm08:8331132, Gm08:8331181,Gm08:8331408, Gm08:8331827, Gm08:8332651, Gm08:8332685, Gm08:8332957,Gm08:8343167, Gm08:8345187, Gm08:8345720, Gm08:8346030, Gm08:8346050,Gm08:8346352, Gm08:8346726, Gm08:8347799, Gm08:8348022, Gm08:8348028,Gm08:8349925, Gm08:8350122, Gm08:8350277, Gm08:8351061, Gm08:8351503,Gm08:8352313, Gm08:8352743, Gm08:8353341, Gm08:8355175, Gm08:8360133,Gm08:8363193, Gm08:8363888, Gm08:8364195 or a marker closely linkedthereto; or (c) can be any marker associated with the rhg4 locus onlinkage group A2.

In other embodiments, two or more marker loci are detected in themethod. In a specific embodiment, the germplasm is a soybean variety.

In other embodiments, the method further comprises crossing the selectedfirst soybean plant or first soybean germplasm with a second soybeanplant or second soybean germplasm. In a further embodiment of themethod, the second soybean plant or second soybean germplasm comprisesan exotic soybean strain or an elite soybean strain.

In specific embodiments, the first soybean plant or first soybeangermplasm comprises a soybean variety. Any soybean line known to the artor disclosed herein may be used. Non-limiting examples of soybeanvarieties and their associated soybean cyst nematode resistance allelesencompassed by the methods provided herein include, for example, Pekingand PI437654.

In another embodiment, the detection method comprises amplifying atleast one marker locus and detecting the resulting amplified markeramplicon. In such a method, amplifying comprises (a) admixing anamplification primer or amplification primer pair for each marker locusbeing amplified with a nucleic acid isolated from the first soybeanplant or the first soybean germplasm such that the primer or primer pairis complementary or partially complementary to a variant or fragment ofthe genomic locus comprising the marker locus and is capable ofinitiating DNA polymerization by a DNA polymerase using the soybeannucleic acid as a template; and (b) extending the primer or primer pairin a DNA polymerization reaction comprising a DNA polymerase and atemplate nucleic acid to generate at least one amplicon. In such amethod, the primer or primer pair can comprise a variant or fragment ofone or more of the genomic loci provided herein.

In one embodiment, the method involves amplifying a variant or fragmentof one or more polynucleotides comprising SEQ ID NOS: 13, 14, 15, 16,17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34,35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52,53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70,71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88,89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104,105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118,119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132,133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146,147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160,161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174,175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188,189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202,203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216,217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230,231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244,245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258,259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272,273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286,287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300,301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314,315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328,329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342,343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356,357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370,371, 372, 373, 374, 375, 376, 377, 378, 379, 380 or variants orfragments thereof.

In one embodiment, the primer or primer pair can comprise a variant orfragment of one or more polynucleotides comprising SEQ ID NOS: 13, 14,15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50,51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68,69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86,87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103,104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117,118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131,132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145,146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159,160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173,174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187,188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201,202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215,216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229,230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243,244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257,258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271,272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285,286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299,300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313,314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327,328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341,342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355,356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369,370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380 or complementsthereof.

In specific embodiments, the primer or primer pair comprises a nucleicacid sequence comprising SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8 or variantsor fragments thereof.

In a specific embodiment, the primer pair comprises SEQ ID NO:1 and SEQID NO:2.

In another embodiment, the method further comprises providing one ormore labeled nucleic acid probes suitable for detection of each markerlocus being amplified. In such a method, the labeled nucleic acid probecan comprise a sequence comprising a variant or fragment of one or moreof the genomic loci provided herein. In one embodiment, the labelednucleic acid probe can comprise a sequence comprising a variant orfragment of one or more polynucleotides comprising SEQ ID NOS: 13, 14,15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50,51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68,69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86,87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103,104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117,118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131,132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145,146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159,160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173,174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187,188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201,202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215,216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229,230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243,244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257,258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271,272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285,286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299,300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313,314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327,328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341,342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355,356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369,370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380 or complementsthereof.

In specific embodiments, the labeled nucleic acid probe comprises anucleic acid sequence comprising SEQ ID NOS: 9, 10 or variants orfragments thereof.

Non-limiting examples of primers, probes, genomic loci and ampliconsthat can be used in the methods and compositions provided herein aresummarized in Tables 1, 2, 3A, 3B and 4, respectively.

TABLE 1  Non-Limiting Examples of Primer Sequences. Linkage SEQ MarkerGroup Marker Primer ID Allele position (ch) Name Name NO Primer Sequence(R/S) 8300131 A2 S07160-1 136868 1 TGTGTTGTGTTTGACTGCCATA C/A   (Gm08)8300131 A2 S07160-1 136869 2 CATTTCCCAAGCCTCTTGAT C/A (Gm08) 8300131 A2S07160-1 100532 3 TCTAGCTCTGACATATTGATGA C/A (Gm08) TTCTTTTGTGTTGT8300131 A2 S07160-1 80588  4 AAGCCTCTTGATAAGACAGTGT C/A (Gm08)CTTCCAAATC 8300131 A2 S07160-1 136870 5 TCTTTTGTGTTGTGTTTGACTGC C/A(Gm08) 8300131 A2 S07160-1 136871 6 TGAGGCTTTCCAGCATCTAAC C/A (Gm08)8300131 A2 S07160-1 136872 7 GGACTGGATCATGAGAATTGG C/A (Gm08) 8300131 A2S07160-1 136873 8 AAGCAGAAGGAGCATTGAGG C/A (Gm08) R=Resistant;S=Susceptible

TABLE 2  Non-Limiting Examples of Probe Sequences. Linkage Marker GroupMarker Probe 1* Probe 2** Position (ch) Name Name Probe 1 Sequence NameProbe 2 Sequence 8300131 A2 S07160-1 102389 ATTCCTAAAGATAGT 102390CTAAAGATACATGCA (Gm08) CCAAT (SEQ IDNO: 9) AGTC (SEQ ID NO: 10) *Probe 1detects the susceptible allele. **Probe 2 detects the resistant allele.

TABLE 3A Non-Limiting Examples of Genomic Loci Comprising the Various MarkerLoci Provided Herein. Resistant Marker (R) or Marker SEQ SusceptiblePosition Name NO ID (S) Allele Reference Sequence 8300131 S07160-1 13 RTGGAATCTGAGAAGAGACTTGAGAAATGGTACTCTTTGAATCCATGTAAGGTAATCATTGCCACTGGATTCATTGCAAGCACACCTCAAAACATTCCTACCACACTGAAGAGAGATGGAAGTGACTTCTCGGCAGCAATTATGGGTGCTCTATTTAAGGCTCGTCAGGTCACAATTTGGACAGATGTTGATGGTGTGTATAGTGCAGATCCTAGAAAAGGTTTGTTATGCTTCGTACTCTGTCTCTGAGTTAAACAATGAGTGGACTGGATCATGAGAATTGGTTTTTAGTAACCAGAGGGAGTTCTAGCTCTGACATATTGATGATTCTTTTGTGTTGTGTTTGACTGCCATAACATGATGTTTGGATTAAATATAAACAATAATATCCTATGCAGTTAGTGAGGCTGTGATTTGGAAGACACTGTCTTATCAAGAGGCTTGGGAAATGGTGAGTTAGATGCTGGAAAGCCTCAATGCTCCTTCTGCTTGTAAAATTAAGGAGATTAACTTGCAAATTGTCTGTTGTACAGTCTTATTTGGGTGCCAATGTCTTGCATCCCCGCACAATTATTCCTGTGATGCGATATGGCATACCCATTATGATAAGGAACATTCC CA 8300131 S07160-114 S TGGAATCTGAGAAGAGACTTGAGAAATGGTACTCTTTGAATCCATGTAAGGTAATCATTGCCACTGGATTCATTGCAAGCACACCTCAAAACATTCCTACCACACTGAAGAGAGATGGAAGTGACTTCTCGGCAGCAATTATGGGTGCTCTATTTAAGGCTCGTCAGGTCACAATTTGGACAGATGTTGATGGTGTGTATAGTGCAGATCCTAGAAAAGGTTTGTTATGCTTCGTACTCTGTCTCTGAGTTAAACAATGAGTGGACTGGATCATGAGAATTGGTTTTTAGTAACCAGAGGGAGTTCTAGCTCTGACATATTGATGATTCTTTTGTGTTGTGTTTGACTGCCATAACATGATGTTTGGATTAAATATAAACAATAATATCATATGCAGTTAGTGAGGCTGTGATTTGGAAGACACTGTCTTATCAAGAGGCTTGGGAAATGGTGAGTTAGATGCTGGAAAGCCTCAATGCTCCTTCTGCTTGTAAAATTAAGGAGATTAACTTGCAAATTGTCTGTTGTACAGTCTTATTTGGGTGCCAATGTCTTGCATCCCCGCACAATTATTCCTGTGATGCGATATGGCATACCCATTATGATAAGGAACATTCC CA

TABLE 3B Non-Limiting Examples of Genomic Loci Comprising the Various MarkerLoci Provided Herein. SEQ SEQ SNP ID ID Consensus Reference SequenceMarker SNP SNP NO NO r² with r² with (200 by flanking SNP) Name Position[S/R] [S] [R] 8357600 8356824 [S/R] 8356824 [C/G] 15 198 0.857GCCGGGCAACCGCTACTACGGCGGCAATGAATA CATCGACCAGATCGAAAACCTCTGCCGCTCACGCGm08:85 GCCCTCCAAGCCTTCCACCTCGACGCCCAATCCT 6824GGGGCGTCAACGTCCAGCCCTACTCCGGCTCCCC (Rhg4GGCCAACTTCGCCGCCTACACCGCCGTCCTCAAC mutation  CCCCACGACCGCATCATGGGGCTAGATCTCC +C/G from Liu+CTCCGGCGGCCACCTCACCCACGGCTACTACAC et alCTCCGGCGGAAAGAAGATCTCCGCCACCTCCATT NatureTACTTCGAGAG TCTCCCTTACAAGGTAAACTCCA 2012*)CCACCGGCTACATCGACTAYGACCGCTTGGAAGA AAAAGCCCTAGACTTCAGGCCAAAACTCATAATCTGCGGTGGCAGCGCGTACCCTCGCGA TTGGG CCGTTGCGCTTGGAAAATACTTGATGGGGAAAGGGTACAGCCTTGTCACTGGCGGAACGGAGAACCAT G08:835CTTGTTTTGTGGGATCTGAGACCTCTTGGATTGAC 7600TGGTAATATATATAGGATTGGATCTCTACCTTCT (Rhg4 8357600 [A/T] 16 199 0.857GGTTTTGATTTGTTACAAATGTCTATAAATCTGAC mutationTTGTTCGTTGTGTGATTGTTTTGCAGGG+AfI+ATA from LiuAGGTGGAGAAACTCTGTGATCTCTGTAACATTAC et al.TGTTAACAAGAACGCTGTTTTTGGTGATAGCAGT NatureGCCTTGGCCCCTGGTGGAGTGCGAATTGGTAACG 2012)ATCTTACTTCTCTTTTATATGCTACAATACAAATC TTGCTTTACTAACTCAATTGGAAACAAGATCTCATTTATAAGATTATAAAAATGATTTCC CATATCGCATCACAGGAATAATTGTGCGGGGATGCAAGACATTGGCACCAAAATAAGACTGTACAAC AGACAATTTGCAAGTTAATCTCCTTAATTTTACAAGCAGAAGGAGCATTGAGGCTTTCCAGCATCTAA Gm08:830CTCACCATTTCCCAAGCCTCTTGATAAGACAGTG 0131 8300131 [A/C] 17 200 0.818 0.738TCTTCAAAATCACAGCCTCACTAACTGCATA[A/C] (S07160-GATATTATTGTTTATATTTAATCAAAACATCATGT 1) TATGGCAGTCAAACACAACACAAAAGAATCATCAATATGTCAGAGCTAGAACTCCCTCTGGTTACTA AAAACCAATTCTCATGATCCAGTCCACTCATTGTTTAACTCAGAGACAGAGTACGAAGCATAACAAA CCTTTTCTAGGATCTGCACTATACACACCATTAGGATGTTTTTCAAATACACTCTTTTCTCGCTGT TTAAAAAAAAAAATACACTCTCTTCTAATAATTAAAAGTTATTAAAAATCATAAATTTGAATGGATCT CATTTTTCATTGAGTAACTCTCTCTCGTGATTTTATATTATCTCTGTGCTTTTTATTTTTTATTTTTAAAA Gm08:825 8257778 [A/T] 18 201 0.8570.679 AATATGTAAAAACCAAGAAACATAAT[A/T]AATG 7778TGSTTCATCTTAATAAAACACTTCTTTCATCCTTA AATATAAGACTTTTATAATTAATTCACACTTATTAATAAAATTACAAAGACTTTTATAATTAATTCACA CTTATTAATAAAATTGCTCGATTTAGTTAGTAATTAACATTATATTTGTTTGTAATTTTAATATTTTTTA AGATTATCTTTAAAATTATTCATTTTTCAAATACACTCTTTTCTCGCTGTTTAAAAA AAAAAATACACTCTCTTCTAATAATTAAAAGTTATTAAAAATCATAAATTTGAATGGATCTCATTTTTC ATTGAGTAACTCTCTCTCGTGATTTTATATTATCTCTGTGCTTTTTATTTTTTATTTTTAAAAAATATGT AAAAACCAAGAAACATAATWAATGTG[C/G]TTCAGm08:825 8257785 [C/G] 19 202 0.848 0.68 7785TCTTAATAAAACACTTCTTTCATCCTTAAATATAA GACTTTTATAATTAATTCACACTTATTAATAAAATTACAAAGACTTTTATAATTAATTCACACTTATTA ATAAAATTGCTCGATTTAGTTAGTAATTAACATTATATTTGTTTGTAATTTTAATATTTTTTAAGATTA TCTTTAAAATTATTCAGACTAAATCTTTAAAATTATTCAGACTAAATATATATTTTTT TCATTTAATTATTTTCTACCCAAACAATTAACATATGAAAAGAGAATAATAGTAGTCGAGTTTTAATTT TAAAATTAAATCCTTCAATTCTCCAATCCTCCCACGAAAGAGAAAATGACAATTCATAGCAATTRTTAT Gm08:825TTATAGACTACAACAACTAGGGGTATT[A/C]TAGT  8163 8258163 [C/A] 20 203 0.8430.681 AAAAAGAAAAACAAGTAATGCAAGAAAGAAGTCTTATACAAAAGAACAAAGAATTTTTTAAATAATG TCTTATATTCATAGACGAAAGAAACAATTGATCCTTTATCATTTTTATTAAACAATAAATGCATAGAT GTAAATAAATTAAAGATTAGAAAAAAGTAAGAACATAATTGGCAAAAAAATAATTAATGTC TAAAAAAAGAAAACGTGGGAGAGTGCAATTAGGATAAAGGGATTGGATTACTTGAAGAAAAAAARA ATAAAGGGGTTAGAAAAAGACCCTCTAGAAGTATACGACAGCCTAAATTGAAATTGGGATACATAGT TTGGACTGTAATAGAATTGTGGATCTGTTTGCTCGm08:825 GTTTTATTTCAAAATAAAACAAAATAAAGAACT+ 8688 8258688 [C/G] 21 2040.895 0.688 C/G+ CTAGCATRACAACAAAAAGTACTAATTTTTAATCTCAAKGATC RGAAC TTTGC RTTTC TTTC CC GTATCTTGTCGAATTTTYATTGTAAGAAATATTCTTT GTGGGTTCAGTTATTCACCATTATTATTTCAGAGGGAGCGATGGGWGGAATTATAATACTTCTTCATC AGATTCAATTTTGATAAAGAAAATCATTCAAAAGAAAAAAARAATAAAGGGGTTAGAAAAAGAC CC TCTAGAAGTATAC GACAGCC TAAATTGAAATTGGGATACATAGTTTGGACTGTAATAGAATTGTGG ATCTGTTTGCTCGTTTTATTTCAAAATAAAACAAAATAAAGAACTSCTAGCATRACAACAAAAAGTA Gm08:825 8258742 [G/A] 22 205 1 0.587CTAATTTTTAATCTCAAKGATCRGAACTTTGC +A/ 8742 G+TTTCTTTCCCGTATCTTGTCGAATTTTYATTGTA AGAAATATTCTTTGTGGGTTCAGTTATTCACCATTATTATTTCAGAGGGAGCGATGGGWGGAATTATA ATACTTCTTCATCAGATTCAATTTTGATAAAGAAAATCATTCAAATAAGAGACTTTATTATCTTCAAA AAGCTAAGTACGGAAGATGCCAAAAAGAAATTGGATCATTTAATTTATGAGGTGTGTGATTTTGT TTCCTAGTTTTTAATTTTGCAAATTGGATCATTTAAGTATTACAGGAATCCAATTTACTCAATTGAATT CTGAAAGATCAAAATTAAATAAATGCAATACCTAAGAGACAAAAAATAATTAATCTATTTTTTTAAAG Gm08:825 8259928 [C/T] 23 206 0.8960.688 AAAATACTACTATCAGATATGGAAGCAC [C/T]AA 9928CAAAACCAGTCCAGGAGAGACATCAGCACCTAC CTACGCACCCCAAAATCAGATACAACTTTAAGCTTACAACATCACCTATAGTAACCTAATATTGCTCA AAATGGAAGCAACCATTCCACAACCAATACAACAAACAAAATCAATAAATTTACTACAAACTAGTCG AAC CGTAC CTC GTTAATGCCATAAACC TAGAC TAAGC TACACAAAC TGAATCAC GTC TAAGAC GCTCTAAAAACAAAATCAGGAGGCAGGTTCCGCA AAATAGGACTGGATAATGATGTTGAAGCAGTAATTTCTATCAAAATTAACAGGAAAAACTCTAAAAA AATCAGC CC CRGGAGAAATTTATATATATTTTTTGm08:826 8260451 [C/T] 24 207 0.818 0.622GTAGATAAAAATTTAAATTAGGGGAAGACACG+C 0451 /T+CTTCTTGTAAAACTACAAGAAAAATTAACAAC ATCAGCATTATAAAATTTATACATCGCATAACAATATGCAAAATCCAAAAATCAATAAACCTAAATTA TTGCTGGTATAACTATTTGACTAAATGTGCCATTGTTGS CCAGAGAATATTAAAATGTAATGAAATAA AGTATTTTAAATTAATTGACTAAGAATTGGCAGC CC CRGGAGAAATTTATATATATTTTTTGTAGATAAAAATTTAAATTAGGGGAAGACAC GYCTTC TT GTAAAACTACAAGAAAAATTAACAACATCAGCATTATAAAATTTATACATCGCATAACAATATGCAA AATCCAAAAATCAATAAACCTAAATTATTGCTGGGm08:826 8260590 [G/C] 25 208 0.918 0.772TATAACTATTTGACTAAATGTGCCATTGTTG[C/G] 0590CCAGAGAATATTAAAATGTAATGAAATAAAGTA TTTTAAATTAATTGACTAAGAATTGGCATGGC TATGAGAAATCATGCACTAATTGAGCAAAGATATG ATATATTTTTTATACTTGTCCTAACAATGTACTCCCACTAATTAAGTTACTAATTGAGCACTCCATAAT TTTTTTTGGAAGATGTTCTTTGGACACTGTGTCATGTCTACCAAGTCCGACTAACTTWTCCGTCC ATCAACCATTTTTTAACTGAGAATTGGTATGATATCAAGAGTTAAGAGTTGTGACTGTATTTGGAAAA ATATTTCTTAAAATAAAATGATATTCAAAAAATATATTTTTAATAGTTTTTTCTGCTGATTTTCAGTCT Gm08:826 8261480 26 209 1 0.856ATAATTAAACGAATTTAGATACTCTATAT[G/T]AA 1480AAAAGAGAAAATCATTTTTTCAATAACAGTCCCA AAACTTTTAAATTAAAAAAAATAAAGTAAAATTTATCTTTTATTTTGAATTAAATCAAGACATACTACT ATACCTGATCAGTCCTGGATCGAATTCTCCCAACCAAATCAACTCGCCATAAATACCCTCTTATATCC AGTTAATTAATGGTCCATCTCGTTTTGAAAGAGAAAATCATTTTTTCAATAACAGTCCCAA AACTTTTAAATTAAAAAAAATAAAGTAAAATTTATCTTTTATTTTGAATTAAATCAAGACATACTACTA TACCTGATCAGTCCTGGATCGAATTCTCCCAACCAAATCAACTCGCCATAAATACCCTCTTATATCCA Gm08:826 8261684 [A/T] 27 210 1 0.791GTTAATTAATGGTCCATCTCGTTTTGAAA[A/T]TT 1684TTTTAACCATGAAGTTTTTTTTTAGTTACATGAGG AAAAGAAAGACAAGGGACAACCAAAAAAACTACACGTACTACTAAATTAAGGCAGATCACACTGCCA CTCCCTCTGCACAAAAACTGGTGGCCTCTGCCAGACCACAGCATCAGAACTCAGAAGCATTGGTTGCA TCAGAGTTTTGTTATGGTGTATTTAGAACCAATCCCGACACAACCAGCTCGAAATTTTCCGC ACCGCAGAATGTCGTGATTCTTGTGGCAACCAGAGTTGTTGTTCTTGCTAGCTCTATATTCTTCTCCTG TGTGGCAGTATTGCATCAATGCTACCATGCAGTGTCTAACAAGACTATATCATATATTTATGATAGTC Gm08:826 8262165 28 211 0.919 0.918TCTAATCAATTTTTGAAAAAATTAGAGTC[A/T]TA 2165ATATTTATACATCTCATTTTCTTATAATTCACTTG CATCTTATTTCATTTTTTCCCCTATCATATAACATATCATATTTATTACATTCTCTCTATTTTTATTTTTATTTCTCTCTCCATCTCTCTTCTCTTTTCACCCTAAA ATGGGGGTGAACACTCAACATGTTTTGAAAAATTATTATTAGATTAATATGTATTG GGGTCATCCTTTCACTTGTTTGGTCTACACCACACTCTTGTCTTGGGTCGCTGAGGTGGCGCGTGAGTT TCACCTCCCAACAGCGATGCTGTGGACTCAACCAGCTACGATACTCGACATCTTCTATTACTACTTTCA CGAACACGGTGAATACATCAAAGACAAAATCAAGm08:826 8263213 [G/C] 29 212 0.913 0.09AGACCCCTCGTGTTTCATTGAATTACCAG[C/G]AT 3213TGCCATTGTTGCTTGCACCACGGGACCTACCCTC YTTTTTATTGGGTTCAAACCCTACTATTGACTCTTTCATTGTCCCAATGTTTGAAAAGATGTTTTATGAT CTTGACGTGGAGACAAAGCCCAGAATACTTGTCAACACCTTCGAAGCCTTGGAAGCGGAGGCTCTCAG AGCCGTTGATAAGTTCAACATGATCCTTGTCTTGGGTCGCTGAGGTGGCGCGTGAGTTTC ACCTCCCAACAGCGATGCTGTGGACTCAACCAGCTACGATACTCGACATCTTCTATTACTACTTTCACG AACACGGTGAATACATCAAAGACAAAATCAAAGACCCCTCGTGTTTCATTGAATTACCAGSATTGCCA Gm08:826 8263250 30 213 1 0.678TTGTTGCTTGCACCACGGGACCTACCCTC[C/T]TT 3250TTTATTGGGTTCAAACCCTACTATTGACTCTTTCA TTGTCCCAATGTTTGAAAAGATGTTTTATGATCTTGACGTGGAGACAAAGCCCAGAATACTTGTCAAC ACCTTCGAAGCCTTGGAAGCGGAGGCTCTCAGAGCCGTTGATAAGTTCAACATGATCCCAATCGGGCC GTTGATTCCCTCGGCTTTCTTGGATGGTCC CAATC GGGC CGTTGATTC CC TCGGCTTTC TTGGATGGGAAAGATMCTAATGATACTTCATTTGGCGGTGACATCTTC C GC CTC TCTAATGGTTGCAGC GAATGGTTGGACTCGAAGCCAGAGATGTCGGTGGTT TATGTCTCGTTTGGTAGCCTTTGCGTGTTGCCTAAGm08:826 8263611 [C/T] 31 214 0.924 0.682GAC GCAAATGGAGGAAC TTGCACGTGC G[C/T] TA 3611TTAGATTGTGGAAGTCCTTTCCTGTGGGTCATTA AAGAAAAAGAAAATAAGTCACAAGTGGAAGGAAAAGAGGAGCTGAGCTGCATAGAGGAATTGGAAC AGAAGGGGAAGATAGTAAACTGGTGTTCTCAAGTGGAGGTTCTTTCACATGGTTCTGTGGGTTGTTTT GTTACACACTGTGGTTGGAATTCAACCATGAAATGAAGAAATTAGGCGGTGTTTGGAAGAGGT GATGGGGAGTGGAGAGAAAGGACAAGAATTGAGAAACAATGCAGAAAAGTGGAGGGGACTGGCCAG GGAAGCTGTCAAGGAAGGTGGCTCTTCGGATAAGAATCTAAGGGCTTTTTTAGATGATGTTGAAGTT Gm08:826TGACCATATGGCTGTCACATCAGCTTTTCCGTTT+ 4149 8264149 [C/T] 32 215 0.9330.702 C/T+TGAATTTTCCTGTCCGTTTCATTTTTCTTTTCTATTATTGCATTTGCATGACTGAGAATCAAGTGAA ATTTCTTCTATATTAGTTTGAAATTTAAAAATATCTAAATGAGCCATGACTCCATGAGTAGTAATTTTG TGTTATAATTGATATATATATTTTCTCTTAAGTAGTGGCCAAAAATTTAATCTTTATGTAGATG ATGCATC TGGATCTGGTTTC CC TATTCATATTTC CAAAGCTTGCATGCTTTCTGGTTTCCTTGCCAATCA CTGCATGGAACAATCTTACCATCATAGGGCATGCTTCTTTTTTTAAGCTCGCTTGTGGTCTTCTTTTGGTACATATGC TC CC CTCC CCCC TTTTTGTTTATTTTT Gm08:826 8265227 [C/T] 33 2160.933 0.736 GTTTTATGGTTCATAATAGAGTTTA[C/T] TGATGA 5227AATAGCCAAATCATAGAATTAGTAAAATATCATG TACAAGGTCAAAATAGTATTTTTAGTAACCATCTTTTTTTTCTCGTACCTTACATAGAAGCTGACTCAA TGATAAAGGAAACCTAAAAATTAGTTTWAAAAAAACCTTTTGGCCTTTTTGACATMATATATGATATT TTTGTCAAAATATGAGACTTTTTGGTACATATGC TCC CC TCCCC CCTTTTTGTTTATTTTTGTTTTATGGTTCATAATAGAGTTTAYTGATGA AATAGCCAAATCATAGAATTAGTAAAATATCATGTACAAGGTCAAAATAGTATTTTTAGTAACCATCT TTTTTTTCTCGTACCTTACATAGAAGCTGACTCAAGm08:826 8265364 [A/T] 34 217 1 0.824TGATAAAGGAAACCTAAAAATTAGTTT[A/T]AAA 5364AAAACCTTTTGGCCTTTTTGACATMATATATGAT ATTTTTGTCAAAATATGAGACTTTTTTTTTATAAAAAC TAATAAAAAAATATTTTTTATTGGTAAAC CTAGAAC TTAAATTTTAGTTATTTTATTCTTAGAS AAAC CTTACC TAACAAATAATTTAATTCAAATATTT GC CTTTCATTC TATTTTATTTCAC CATATGAGACTTTTTTTTTATAAAAACTAATAAAA AAATATTTTTTATTGGTAAACCTAGAACTTAAATTTTAGTTATTTTATTCTTAGASAAACCTTACCTAA CAAATAATTTAATTCAAATATTTGCCTTTCATTCTATTTTATTTCACCTTAACAACTTCCCTGGCCACAA Gm08:826 8265614 [G/A] 35 218 0.8380.8 CATGTTGGATCTCAGTAAAAATTGATG[A/G]TGTA 5614AGATCATTCCATTAC GAAGAGATGCATGGCC TAT TATTCTTTCTCCATCCAAGAAAAAAATACATTTATTCTTGCTTCCTGTTAAAACATAAAAAGACGTTTT AC CTTAGTATGATAACC TTCATAAATAGTTAAATATAGCATTGTCTTGAACTTTGAAATAAATTATGT TTAATTAGAACTTATAACTATAAGTATATGTCAAGTATTATAATAAATATTTAATTATA TAAATAAATAATTTTATTCTTAAATATAAACATTTACAAAGTTAAAGTAACAAAAAAGTAAGTTTTTA ATTCTCTTAATAATGTCATATCCTAATTTCGTACTAGGACTATCATTCGTCAACGTTTTGATTCTCCATT Gm08:826 8266183 36 219 0.924 0.773GTCAAATTGAATTGTTCGACACCAGTTG[C/T] TRT 6183GTAAGACGGAAGATTATTCGACATTTCAGTAAAG AATGCAAAAAATGCCCAAATGGAAGGACAAAAGGATCATTTTRAGGC TTTTTCAGACCC CTGACTC GCTCAGGC TAGTC TCTGGC TCAC CTAGGC CC CTAAATAGTTTAGGGGTGAAGTAACTAGCTCGYCTGGAC GAGCAAGGTTACTTCAGGTTGAAGCAAATGTCAAGTATTATAATAAATATTTAATTATATA AATAAATAATTTTATTCTTAAATATAAACATTTACAAAGTTAAAGTAACAAAAAAGTAAGTTTTTAAT TCTCTTAATAATGTCATATCCTAATTTCGTACTAGGACTATCATTCGTCAACGTTTTGATTCTCCATTGT Gm08:826CAAATTGAATTGTTC GACACCAGTTGYT [A/G] TGT 6185 8266185 [G/A] 37 220 0.9240.773 AAGACGGAAGATTATTCGACATTTCAGTAAAGAATGCAAAAAATGCCCAAATGGAAGGACAAAAGG ATCATTTTRAGGCTTTTTCAGACCCCTGACTCGCTCAGGCTAGTCTC TGGC TCAC CTAGGCC CC TAAATAGTTTAGGGGTGAAGTAACTAGCTCGYCTGGACG AGCAAGGTTACTTCAGGTTGAAGCAACAGTAACAAAAAAGTAAGTTTTTAATTCTCTTAATA ATGTCATATCCTAATTTCGTACTAGGACTATCATTCGTCAACGTTTTGATTCTCCATTGTCAAATTGAAT TGTTCGACACCAGTTGYTRTGTAAGACGGAAGATTATTCGACATTTCAGTAAAGAATGCAAAAAATGC Gm08:826 8266263 [A/G] 38 221 0.9040.816 CCAAATGGAAGGACAAAAGGATCATTTT [A/G] AG 6263GC TTTTTCAGACC CC TGAC TC GC TCAGGC TAGTC TCTGGC TCACC TAGGCC CC TAAATAGTTTAGGGGT GAAGTAACTAGCTCGYCTGGACGAGCAAGGTTACTTCAGGTTGAAGCAACARCTC GC TTGGGTGAGCTCCAGATCAAC TAAGTC CC CTCATTTCC TATAAA TAGGCATGAGGGGCTGAAAGAAAGGGTTCCATTGTCAAATTGAATTGTTCGACACCAGTTGY TRTGTAAGACGGAAGATTATTCGACATTTCAGTAAAGAATGCAAAAAATGCCCAAATGGAAGGACAA AAGGATCATTTTRAGGC TTTTTCAGAC CC CTGACTCGC TCAGGC TAGTC TCTGGC TCACC TAGGC CC C Gm08:826 8266350 39 222 10.895 TAAATAGTTTAGGGGTGAAGTAACTAGCTCG+C/T 6350+CTGGACGAGCAAGGTTACTTCAGGTTGAAGCAA CARCTCGCTTGGGTGAGCTCCAGATCAACTAAGTCCCCTCATTTCCTATAAATAGGCATGAGGGGCTG AAAGAAAGGGTTCARCCTTCARATATTGAAAGGATTTAGTGAAATTTGAAGAAAAGAAGAARAAAT AAAGGAAAAACAAGGTCGAGGTGCTACCGAATCTGTAAGACGGAAGATTATTCGACATTTCAGTAAA GAATGCAAAAAATGCCCAAATGGAAGGACAAAAGGATCATTTTRAGGC TTTTTCAGAC CC CTGACTC GCTCAGGC TAGTC TC TGGCTCACC TAGGC CC CTAAATAGTTTAGGGGTGAAGTAACTAGCTCGYCTGGA Gm08:826 8266386 [A/G] 40 223 1 0.824CGAGCAAGGTTACTTCAGGTTGAAGCAACA[A/G] 6386CTC GC TTGGGTGAGC TCCAGATCAAC TAAGTC CCCTCATTTCCTATAAATAGGCATGAGGGGCTGAAA GAAAGGGTTCARCCTTCARATATTGAAAGGATTTAGTGAAATTTGAAGAAAAGAAGAARAAATAAAG GAAAAACAAGGTCGAGGTGCTACCGAATCACGATCGTAATCGATTTTCACATCGTTCTTCGTTCG CAGACCCCTGACTCGCTCAGGCTAGTCTCTGGCTCACCTAGGCCCCTAAATAGTTTAGGGGTGAAGTA ACTAGCTCGYCTGGACGAGCAAGGTTACTTCAGGTTGAAGCAACARCTCGCTTGGGTGAGCTCCAGAT CAACTAAGTCCCCTCATTTCCTATAAATAGGCATGm08:826 8266473 [G/A] 41 224 0.918 08GAGGGGCTGAAAGAAAGGGTTCARCCTTCA[A/G] 6473ATATTGAAAGGATTTAGTGAAATTTGAAGAAAA GAAGAARAAATAAAGGAAAAACAAGGTCGAGGTGCTACCGAATCACGATCGTAATCGATTTTCACAT CGTTCTTCGTTCGTCATCCGGTTAGTATTTATTTTAAGTATTTCAATTCAATCTATGCACCCATAAGGG TCTTCTTTGTCGATTCATGCATCTTCATCTCTGTAATCTATTTTCTTTTGGTAAAGTGAGTTTTGA CCGGTCATTTACGTCACCAAACATCTTTTAATTAGTTTGAAGTTTAATAAGTGAAATCAAGTTAAAAT CAACATGTAACCGAGCTTTTTATCCGCAAAATTCACTTAAATCCGTTCAAGGTCCAAGGCCTTAATGG Gm08:826TCTCTTTTATTTTTGTTGGTTCGAATGAA[C/T]TTT 6888 8266888 42 225 0.924 0.08TCAAAAGTTTAAAATCAACTCGACACGCAATTTT CTTGTTTTAAGAACTATGTAGGTCTGAGTTTCTCATCGCAMTTGAGGATACGTAGGAGCAAGGGCAAC GCCTTTGTCGACCCGAAAAAATAAAGAAGCATAAAAAGGGAAAATAAGTAATATTGAAGTCACGTT TTTGCACATTCGATTAAAGGTTGTCRTCCGAAYTTTTCAAAAGTTTAAAATCAACTCGACACG CAATTTTCTTGTTTTAAGAACTATGTAGGTCTGAGTTTCTCATCGCAMTTGAGGATACGTAGGAGCAAG GGCAACGCCTTTGTCGACCCGAAAAAATAAAGAAGCATAAAAAGGGAAAATAAGTAATATTGAAGT Gm08:826 8267085 [A/G] 43 226 0.9120.808 CACGTTTTTGCACATTCGATTAAAGGTTGTC[A/G] 7085TCCCCTGTGACGAAYACGTGGGGTGTTAATACCT TTTTCGCTCGTAAATAACTCCCGTACCCTTATTTTCAAAATTCGCAKATCCCCCTTTTTGGTTTTTCTAA CGTTTTCCTCGAATAAACGTTGGTGGCGACTCCCGCGTGTTTTTCTTTTTGGAAGACGCATCCTTGAGT CTCGCCTCACCCCTCCCGTCGAAGGGTMTTGAGGATACGTAGGAGCAAGGGCAACGCCTT TGTCGACCCGAAAAAATAAAGAAGCATAAAAAGGGAAAATAAGTAATATTGAAGTCACGTTTTTGCA CATTCGATTAAAGGTTGTCRTCCCCTGTGACGAAYACGTGGGGTGTTAATACCTTTTTCGCTCGTAAA Gm08:826 8267166 44 227 1 0.836TAACTCCCGTACCCTTATTTTCAAAATTCGCA+G/T 7166+ATCCCCCTTTTTGGTTTTTCTAACGTTTTCCTCGA ATAAACGTTGGTGGCGACTCCCGCGTGTTTTTCTTTTTGGAAGACGCATCCTTGAGTCTCGCCTCACCC CTCCCGTCGAAGGGTAGGTTGCAACAGATAATAATAAAAAAATTCAACCATGATATTCGCAACAATAA ATTAAATGCACACATACATATATATAGTGAATTAGTGTGAGTCTCAGATTCTTCAAATGGTC TATGAGTTCATATTCATGCAGTAAYGTCTCACTGCTTTTCTTATCATATATGAAAGTATTCAAAATCTC TTCTTCATCCTAGATGGAGGTATCTATAACTTCATCTCCATCCCAAATGAAGGTGTCTCGTACATATTC Gm08:826 8267721 [C/T] 45 228 0.8170.772 AATTCTCAAAATAAAACATAAATTGTCA[C/T]TAC 7721TTCCTAAAGGATGATAACCAATTCACACATATTT ATAAAATATCATTTCAAATAACTATCAAATAAATACTTTAATTCCATATACACTAATTAATAACTTGSA AGGTCATACCTTAGTTATAGCATCACGTAAGTCAATTTATAATTAACTATGAAATAAAACATACACAC AAATTAAAATATATTTTAGTTGCTATCTTCATCCTAGATGGAGGTATCTATAACTTCATCT CCATCCCAAATGAAGGTGTCTCGTACATATTCAATTCTCAAAATAAAACATAAATTGTCAYTACTTCC TAAAGGATGATAACCAATTCACACATATTTATAAAATATCATTTCAAATAAC TATCAAATAAATAC TT Gm08:826 8267826 [G/C] 46 229 0.8310.824 TAATTC CATATACAC TAATTAATAAC TTG[C/G]AA 7826GGTCATACCTTAGTTATAGCATCACGTAAGTCAA TTTATAATTAACTATGAAATAAAACATACACACAAATTAAAATATATTTTAGTTGCTATATATGATAG CTAAACACAAAATCCAAACAAGCTGATTGATGAATTTTCAAATAAATTTTAAGATTGAATATGCAAC TAGTGAATATTTGTACATTGTAATACCTTATCTAGTTTCTATCGTGCATATTTGTTGAAGTTAA ACACAAGATCCAAGYAAGCACATATGATGCATTATAATTGCAC TAAAATTTGAATATAGTTTC TATA TATCGTGCATGTTTGTTGGCTCTCCTTGACAAGCATATCTATTTAATTTATACAAGTAGTAAATAAAAT Gm08:826GATAAGACTAAATGATGAGTTCACATATA[C/T] TT 8336 8268336 [C/T] 47 230 0.8290.561 TATTTGTACTCWTATATATATATATATATATAATTCTTGGATGGAAAGGAC CC CGAAGATAC TTC CTTGGGTGGTGACTTGTTACCGGTTTCAAATGGTTACG TTGAGTGGCTTGACTCAAAGGAAGACAAGTCCGTGGTTTACATTTCATTTGGGAGCTACTTTGTGTTGT CTAAGAGACAAACGGAGGAAATTGCACAGGTGGAGGTTCAGTGGGTTGTTTTGTGACGCA CTGTGGTTGGAATTCGACCATGGAGAGCTAGGTTTCGGGGGTGCCCATGGTGGTGTTTCCTCAGTGGT CGTACCAAAAGACAAATGCTAAACTGATAGAAAATGTGTGGAAGATAGGGGTGAGGGTGGATCATG Gm08:826 8268861 [A/C] 48 231 1 0.722AGGATGGGAAAGTAGAAGGAGAAAGAGATTAA+ 8861 A/C+AAGTGTTC GGAAGAGGTGATGGGGAGTGGA GAGTTGAGAATGAATGTAAAGAAATGGAAGGGTTTGGCCAGGGAGGCAGC CAAGGAAGGTGGTC CT TCAGATTTCTTGATGCCATGACGTTGCAGAATCGATAATCAATGCACGTGTTTGCCAAATAATTGACT TGGATTCCCGTGTTCTCAGTTCTTCCATGCTAAAT TAGGTGGTC CTTCAGATTTC TTGATGCCATGAC GT TGCAGAATCGATAATCAATGCACGTGTTTGCCAAATAATTGACTTGGATTCCCGTGTTCTCAGTTCTTCCATGC TAAATTATTC TTTTTC TGCTTC TWTTTC TTTTTCCAATCAATTGATTCTATGTTTAAGATTTTTA Gm08:826 8269148 49 232 0.842 0.627TTATTTAGAACAATTAAATTATTATTG[C/T]TTTA 9148AGAGATAGTATTATTTTAAGTTTAAATGTATATTT TTTATTCATAATTATATCTCTATTTAATCTGGTATAC TCC TTAAAATTAC TTTTATTTAATTATGTTTTTTTTTAAAATAATCAAATTATTCAATCTTATTGATA AGTGGTTTGTATCAAATGCTCACCTAAAAAAGATAAATAGACTCCCAAATATTAGA AGATAATTAATTTCTTTTAAATGGATGTAGGAAGAGACTAAATTATTACTAATCTTATTGCTTTATATT TTTTATAGTTATCTTTCCACTCCTACAGTACGAAACACATGTAATAAATCAGTGCCATTAACATACAAC TCGACCTAATTGTAATTTGTAGTAACTTAGATAGGm08:826 TTTAGATTTTTTTTTTGTTATGGTATTA[C/T] GTAT 9785 8269785 [T/C] 50233 0.912 0.808 TTCATAAAAATTTATATTAATTTTCTTTTGAAAAATATTATACWTCATATTGTCTTCTTGCCTTTGTAAA ATAAAAGTGTTAAAATATCAATACTYATGTTTATTTGAACAAGTGAGATGCATGTAATC RC TATCATT ATTTAGGAATGYTAATGAACCTACTTGTTGCACTAATTAAGCYTGTTTCAACCTGTAA TATTGTCTTCTTGCCTTTGTAAAATAAAAGTGTTAAAATATCAATACTYATGTTTATTTGAACAAGTGA GATGCATGTAATC RC TATCATTATTTAGGAATGYTAATGAACCTACTTGTTGCACTAATTAAGCYTGT TTCAACCTGTAAAAAAAAGTCTGTTTCAAAATTAGm08:827 8270037 [G/T] 51 234 0.924 0.823TTTTTTATGCATTTTACTTAAAAAAATTA[G/T] AC 0037CTAATGAATTTTGAATATTGATTTGATTTTTTTAA GAGAATATATTTTTGAGTTATATATATATATATTAGTAGTCCTACCTCGTTCTAATATTTTATATTTTTT TAATAAAATATACAAATTTTTAAACAATTTTGTATTAAGGAAAAATTAATCATTTTATTMTTATAATT ATACAAAATTTAGCTTTGAATGACCAATGAAAGTTTGAATATAAAAGGTTACTTTGTTT AAACTTAAAAAAAAATTCTAAAAAATATTTTTTAAGAAGTAAATATGATTTATTTATTAACAAGACAT TTTTCTATTTTTAAGAAAAAAATACATAAAAAATAATTATTTTATTAAAAAATGATC CAAAC CC TTCA Gm08:827 8270562 [C/A] 52 235 10.704 TCATTAATGTTAATGATTAATCTATTAATT [A/C] A 0562TGTTTAATTTATTATATTATAATTATAATAGATTA TACAAAAAGCAATTATACGATTTAATGTTTTATATATTTAATTTTATATTTAARATGTGGAAGATGC GT TAGCAAGTATTAAGATATTGACTAAAAAAGAAAATTAAAAAATATATAATTAAAACTAAAGCATTTT CTATAAATAAAAAATATAAGACTTTTTTTTAACAAGACATTTTTCTATTTTTAAGAAAAAAA TACATAAAAAATAATTATTTTATTAAAAAATGATCCAAACCCTTCATCATTAATGTTAATGATTAATCT ATTAATTMATGTTTAATTTATTATATTATAATTATAATAGATTATACAAAAAGCAATTATACGATTTAA Gm08:827 8270652 [A/G] 53 236 1 1TGTTTTATATATTTAATTTTATATTTAA[A/G]ATGT 0652GGAAGATGCGTTAGCAAGTATTAAGATATTGACT AAAAAAGAAAATTAAAAAATATATAATTAAAACTAAAGCATTTTCTATAAATAAAAAATATAAGACT TTTTTTTTACATGACATATAAAACTTACTCTATTCAATATTAAAATTGTTAAAGATTTAACTGGTATAT AC TAATAGTGTAAATATATTTTACACTCAMATATTGATTCATCATGTAGTGAAAAACTAA TCWCTTTTACTCAACCTAAS CTGTATCGATGYTAATCATTGCTCTTAGTACATTGATTATAAAAAAAA TACTAGAAAGATAAAGTTTTTGTTAGAAATCATTTGCGAGTATATTTTAAAATAATTGAAGAATACAT Gm08:827 8271540 54 237 1 0.419TTTTATGCATTATATAGTTAAAGTGTTTTT [G/T] TT 1540TTCCTTTTTTCACTTCCTCTATTTTAACCACTATTT TCTTTCTACACAMAAAAAAAAATCCATCATTTTTCTTTTATCCTTTTAACAAATTTTGGTTTTGGACAG TRAACACACACAAAATATATATTTYTCTTCTAATATGATTTGTTTTATTTTTGATGCCAATATGTTATG ATTGTTTGATAATGTAAAAAATATAAS CTGTATCGATGYTAATCATTGCTCTTAGTAC ATTGATTATAAAAAAAATACTAGAAAGATAAAGTTTTTGTTAGAAATCATTTGCGAGTATATTTTAAA ATAATTGAAGAATACATTTTTATGCATTATATAGTTAAAGTGTTTTTKTTTTCCTTTTTTCACTTCCTCT Gm08:827 8271591 [C/A] 55 238 0.9190.625 ATTTTAACCACTATTTTCTTTCTACACA[A/C]AAA 1591AAAAAATCCATCATTTTTCTTTTATCCTTTTAACA AATTTTGGTTTTGGACAGTRAACACACACAAAATATATATTTYTCTTCTAATATGATTTGTTTTATTTTT GATGCCAATATGTTATGATTGTTTGATAATGTAAAAAATATTAS AC TAATAATGC GTAGTAC TAGYAA TTAACCTCATTTTTWAAATAGTTAAAGATAAAGTTTTTGTTAGAAATCATTTGCGAGT ATATTTTAAAATAATTGAAGAATACATTTTTATGCATTATATAGTTAAAGTGTTTTTKTTTTCCTTTTTT CACTTCCTCTATTTTAACCACTATTTTCTTTCTACACAMAAAAAAAAATCCATCATTTTTCTTTTATCC Gm08:827 8271649 [A/G] 56 239 1 0.895TTTTAACAAATTTTGGTTTTGGACAGT[A/G]AACA 1649CACACAAAATATATATTTYTCTTCTAATATGATTT GTTTTATTTTTGATGCCAATATGTTATGATTGTTTGATAATGTAAAAAATATTASACTAATAATGCGTA GTACTAGYAATTAACCTCATTTTTWAAATAGTTAAAAGAACTTGCTCATTCATTATTAATTTTTCATTA AAAATATTGTACCGGCCACTTTACATTTGCGAGTATATTTTAAAATAATTGAAGAAT ACATTTTTATGCATTATATAGTTAAAGTGTTTTTKTTTTCCTTTTTTCACTTCCTCTATTTTAACCACTAT TTTCTTTCTACACAMAAAAAAAAATCCATCATTTTTCTTTTATCCTTTTAACAAATTTTGGTTTTGGAC Gm08:827 8271672 57 240 1 0.824AGTRAACACACACAAAATATATATTT[C/T]TCTTC 1672TAATATGATTTGTTTTATTTTTGATGCCAATATGT TATGATTGTTTGATAATGTAAAAAATATTASACTAATAATGCGTAGTACTAGYAATTAACCTCATTTT TWAAATAGTTAAAAGAACTTGCTCATTCATTATTAATTTTTCATTAAAAATATTGTACCGGCCACTTTA ATTTATTTTCAAATGCTATTAAAGTAGTACTAGYAATTAACCTCATTTTTWAAATAG TTAAAAGAACTTGCTCATTCATTATTAATTTTTCATTAAAAATATTGTACCGGCCACTTTAATTTATTTT CAAATGCTATTAAAATAAAGCAATGAGTTAATGACATTAATTAAGAAATGCATTTAAAATTTTATTAA Gm08:827 8271955 58 241 0.09 0.847TATTAAGGATCTTGTTAATTAATGTTTT[C/T]CCCC 1955CACAAGTCTTCTCTTTCAAAGGCCTAATGTACAT TAGGACACTAAATGTCACCCCTTTAAATGAATATTCAAACATTGATTCATCACTTAGTGAAAARTTAA TCTCTTCCACTTGACTCAACCGGTGCTGATGTTAACCATTGCTCTTAATATTGGTTATAAAAAATAATA AAAAGATAAAGTTTTTGTTAGAAATACCCAACGGTGCTTGTGAACACCTTTGAAGCTTT GGAAGAAGAAGCGTTGAGGGCCATTGATAAGATCAACATGATCCCCATCGGGCCGTTGATTCCTTCT GCGTTCTTGGACGGGAATGACCCAACTGATACTTCGTTTGGTGGGGACATTTTTCAAGTCTCAAATGA Gm08:827 8273257 [G/A] 59 242 0.9330.721 TTACGTTGAATGGCTTGACTCAAAGGAAGAG+A/G 3257+ATTCGGTGGTTTACGTTTCATTTGGTAGCTACTT TGAGCTTTCTAAGAGACAAATGGAGGAAATTGCACGTGGGTTATTAGATTGTGGACGTCCATTYTTG TGGGTCGTTAGAGAAAAGGTAATTAATGGAAAAAAAGAAGAGGAGGAGGAGCTTTGTTGTTTCAGA GAGGAATTGGAGAAGTGGGGGAAGATAGTGACATCTGCGTTCTTGGACGGGAATGACCCAACTGATA CTTCGTTTGGTGGGGACATTTTTCAAGTCTCAAATGATTACGTTGAATGGCTTGACTCAAAGGAAGAGR ATTCGGTGGTTTACGTTTCATTTGGTAGCTACTTTGAGCTTTCTAAGAGACAAATGGAGGAAATTGCA Gm08:827 8273355 60 243 0.854 0.825CGTGGGTTATTAGATTGTGGACGTCCATT[C/T]TT 3355GTGGGTCGTTAGAGAAAAGGTAATTAATGGAAA AAAAGAAGAGGAGGAGGAGCTTTGTTGTTTCAGAGAGGAATTGGAGAAGTGGGGGAAGATAGTGAC ATGGTGTTCTCAGGTGGAGGTTCTTTCGCATTCTTCTGTGGGTTGTTTTTTAACACACTGTGGGTGGAA TTCGACCATGGAAAGCCTTGTTTCTGGGGTGCGAAAGAAGGTGGCTCTTCAGAGAAGAATCTG AGGGCATTTGTGGATGATGTTAGACAAAAATTTATGCATACACATGTGGGTGAATATTAATTAAGTTC GTCTCTAACTAGCTAGTAGTAAGCTGTAATGTGTTATTGTATGCTTATGATGCATGGCTTCAAACATT Gm08:827 8273979 [A/C] 61 244 0.870.734 GAAAGATGAACTGAAAAAATTAAGAAATTAT+A/ 3979C+AGTCAGTTAATAAAAATGTGCGAAAATGGAAT ATCTTCAATAATAACATGTGCGTRTTGCTAAAAAATGAGTTGTTGTCACGTTAGATGGTGGATGCCAT ATAACTGTCCAATATGTTGCCCAATTCGTCAGGAAAAGATAAATATTTTGATAAAGATTATTATTACA TTGTTGCTTTATACTCCCTTCCTTTCTTTTTATGAAATGTCAATCAAAATATACAACAGTATGTGC ATGGATTCTTGATGACAATAATTCCAAAACCACAAATATGTATTTATAATCATCTTAAAAGCTCTAGT GAGACACTTAGCKGTACAAATTAAATTTTTTAAATCGTTGGGCAAAGAATCATCAGCAAATGTAGTTT Gm08:827 8275766 62 245 0.928 0.903TTTTTTTTTTTTGAGAAATCACCCAATGTA[G/T]TC 5766AATTGCGGAAGSAGGAGCTTGTCATTCCAGTAGT CCAATTTTTCAGTTATACTTTTGATTTTTATAGGGTAAGTACTAAGTAACCTAGCTAGTTTCTTAATCT CATGATCTCTTGGCTTATYTTTTTTTTTTTTWAATTTGTGCTTGAGTCACTATACATATTTACTTGGTTG TCGAACAAAATTAAAATYTCTTCGTAAATATACAACAGTATGTGCATGGATTCTTGATG ACAATAATTCCAAAACCACAAATATGTATTTATAATCATCTTAAAAGCTCTAGTGAGACACTTAGCKG TACAAATTAAATTTTTTAAATCGTTGGGCAAAGAATCATCAGCAAATGTAGTTTTTTTTTTTTTTTGAG Gm08:827 8275780 [C/G] 63 246 0.9240.823 AAATCACCCAATGTAKTCAATTGCGGAAG[C/G]A 5780GGAGCTTGTCATTCCAGTAGTCCAATTTTTCAGTT ATACTTTTGATTTTTATAGGGTAAGTACTAAGTAACCTAGCTAGTTTCTTAATCTCATGATCTCTTGGC TTATYTTTTTTTTTTTTWAATTTGTGCTTGAGTCACTATACATATTTACTTGGTTGTCGAACAAAATTA AAATYTCTTCGTACCTAAACAAAACCCAATGTAKTCAATTGCGGAAGSAGGAGCTTGTCA TTCCAGTAGTCCAATTTTTCAGTTATACTTTTGATTTTTATAGGGTAAGTACTAAGTAACCTAGCTAGT TTCTTAATCTCATGATCTCTTGGCTTATYTTTTTTTTTTTTWAATTTGTGCTTGAGTCACTATACATATTT Gm08:827 8275959 64 247 0.929 0.837ACTTGGTTGTCGAACAAAATTAAAAT[C/T]TCTTC 5959GTACCTAAACAAAACCTAACTTAAAGTCCCAGAC TAATTCAACAATAATCAACTCAATTTTTTTTTTTTTGCATGTTACATTTCATACATTAACTGTTGAGCTA CTTTATGGGTTCCCTCCCGTGTAGGGTTTGTTTAATGATATTAGCTTGAAGTTTTCACTCTTTTGATCTT CAAGAAGAGTTAAAGGTGGACGCAACTTGAGGCTGAACTCGGTCGTGCGGTCAAG CAAGACATTTCTGTGTACGTAGCTGTACAATAATATACAATGAATTAGAATAATAACAGATTATGTGG CATTAATTATTACAGCAGCAACTCATTCCTTGATTCTGGGAATTAGCAATTTCTTCCAGCTTATATATAT Gm08:827 8276701 65 248 0.874 0.923ACCAGCATCTCAATCCTTGATTGTACGA[C/T]ATA 6701ATTTTGCAATTTGATCCAAATTTATTACAGCTAGT TAGGATACTACTCGTCTTACAATTTTTGACAAGGTTTTGTCAGCAATGTTGAGGATGTTTAAGCTGAA CACCGTCCGAGAAGTAAAATACTATTAAAGGAGGCTAAAGGRATATATTGGATTAGAATTTTAAAAG ATTATTTTAATATAAAAGGTTATATGA Gm08:8278276849 [A/G] 66 249 0.904 0.79 6849 Gm08:827 8276913 67 250 0.684 0.8276913 Gm08:827 8277162 [A/G] 68 251 0.904 0.655 7162 Gm08:827 8277227 69252 0.918 0.743 7227 Gm08:827 8277248 [A/G] 70 253 1 0.824 7248GTTATGGAATGCAATAATAAATATATACTAAAAA AGAGTAATAAGAGTGTGAAATTGGTAY[A/G]ASA71 254 1 0.756 GTTATTAAGTCATGTGGATAATGAAATTAAGAGTAACATTTATGAAAATATTATATTGAGCAAGTTAT AAACATAATCAMTAAAACTCATCATAAGAAAAAAAACATGATTAGTCTTGACACATAAGATAAACAT TAATTTAATTTAAAAAACAAAGRAAAAAGTGTAGAGGGGAGACATATATTTGACATTTTTTA ATTCTCCTATATTAACCTTTCATGCAATAATATCTTCTCATTCTYACTTTTGAATTTGAACAATARATTT AAAATTATACATTGATTTTCTGATTTTTTTAATTAGTCTAATTATTTCATAATAAATATAATGACATGT TATGGAATGCAATAATAAATATATACTAAAAAAGAGTAATAAGAGTGTGAAATTGGTAYRA[C/G]AG 72 255 1 0.755TTATTAAGTCATGTGGATAATGAAATTAAGAGTA ACATTTATGAAAATATTATATTGAGCAAGTTATAAACATAATCAMTAAAACTCATCATAAGAAAAAA AACATGATTAGTCTTGACACATAAGATAAACATTAATTTAATTTAAAAAACAAAGRAAAAAGTGTAG AGGGGAGACATATATTTGACATTTTTTATTATATACTAAAAAAGAGTAATAAGAGTGTGAAAT TGGTAYRASAGTTATTAAGTCATGTGGATAATGAAATTAAGAGTAACATTTATGAAAATATTATATTG AGCAAGTTATAAACATAATCAMTAAAACTCATCATAAGAAAAAAAACATGATTAGTCTTGACACAT AAGATAAACATTAATTTAATTTAAAAAACAAAG+  73 256 0.862 0.648 A/G+AAAAAGTGTAGAGGGGAGACATATATTTGACATTTTTTATTTCAAAAGAATAAGAGAAATATAT ATGGTGCTTGCATCTTGAWGAACATTAAATAGATAARAAGATATGTGTGATAAAAGAAAAAAAAAAG TGTGGTAATCAATAGAAAAAAAAAAGAGWAAAATCATTCAAATCATTCAATAGAAAAGTGTGGGGT TGTTATGAAAATATTATATTGAGCAAGTTATAAACAT AATCAMTAAAACTCATCATAAGAAAAAAAACATGATTAGTCTTGACACATAAGATAAACATTAATTT AATTTAAAAAACAAAGRAAAAAGTGTAGAGGGGAGACATATATTTGACATTTTTTATTTCAAAAGAA TAAGAGAAATATATATGGTGCTTGCATCTTGA+A/74 257 0.895 0.622 T+GAACATTAAATAGATAARAAGATATGTGTGATAAAAGAAAAAAAAAAGTGTGGTAATCAATAGAA AAAAAAAAGAGWAAAATCATTCAAATCATTCAATAGAAAAGTGTGGGGTTGTTTAATTGATGTTTTA TATTAAAAAATTAGATGAAATTCATCCAAATCATTCTTAAAAAATAATGCATCAAAATTTGTATATTT AGCAAGTTATAAACATAATCAMTAAAACTCATCATAAGAAAAAAAACATGATTAGTCTTGACACAT AAGATAAACATTAATTTAATTTAAAAAACAAAGRAAAAAGTGTAGAGGGGAGACATATATTTGACAT TTTTTATTTCAAAAGAATAAGAGAAATATATATGGTGCTTGCATCTTGAWGAACATTAAATAGATAA+ 75 258 0.87 0.53A/G+AAGATATGTGTGATAAAAGAAAAAAAAAAG TGTGGTAATCAATAGAAAAAAAAAAGAGWAAAATCATTCAAATCATTCAATAGAAAAGTGTGGGGT TGTTTAATTGATGTTTTATATTAAAAAATTAGATGAAATTCATCCAAATCATTCTTAAAAAATAATGCA TCAAAATTTGTATATTTTTAAATATTAAAAGACTTTGGTAATCAATAGAAAAAAAAAAGAGWAAAATC ATTCAAATCATTCAATAGAAAAGTGTGGGGTTGTTTAATTGATGTTTTATATTAAAAAATTAGATGAA ATTCATCCAAATCATTCTTAAAAAATAATGCATCAAAATTTGTATATTTTTAAATATTAAAAGACTTTT Gm08:827 8277876 [C/T] 76 259 0.8360.713 TTATAAGTTATAAAAAATTATAATTGAATA[C/T] C 7876ACMAAATTTTATTATTTTTCTTAAAAAATCTTAW ATGTTTTAATTGAATACCATAAGACTTTTTTATATAAAAAHTATTTTAAAATCTTTTMAAATCTTAATC YAATATATCCACTAAGTTATYAAAGGCTAGGAGGAAACAAGTGGASCATGAGACAATACATATATA GGGGGGAATATATGGAAATTGAAAAAAAAAAATCAATAGAAAAAAAAAAGAGWAAAATCATTC AAATCATTCAATAGAAAAGTGTGGGGTTGTTTAATTGATGTTTTATATTAAAAAATTAGATGAAATTC ATCCAAATCATTCTTAAAAAATAATGCATCAAAATTTGTATATTTTTAAATATTAAAAGACTTTTTTAT Gm08:827AAGTTATAAAAAATTATAATTGAATAYCAC [A/C] 7880 8277880 [C/A] 77 260 0.8090.673 AAATTTTATTATTTTTCTTAAAAAATCTTAWATGTTTTAATTGAATACCATAAGACTTTTTTATATAAA AAHTATTTTAAAATCTTTTMAAATCTTAATCYAATATATC CAC TAAGTTATYAAAGGC TAGGAGGAA ACAAGTGGAS CATGAGACAATACATATATAGGGGGGAATATATGGAAATTGAAAAAAAAAAGAT TAGATGAAATTCATCCAAATCATTCTTAAAAAATAATGCATCAAAATTTGTATATTTTTAAATATTAA AAGACTTTTTTATAAGTTATAAAAAATTATAATTGAATAYCACMAAATTTTATTATTTTTCTTAAAAA ATCTTAWATGTTTTAATTGAATACCATAAGAC TTGm08:827 8277969 [C/A] 78 261 0.87 0.658TTTTATATAAAAAHTATTTTAAAATCTTTT +A/C +A 7969AATCTTAATCYAATATATCCACTAAGTTATYAAA GGCTAGGAGGAAACAAGTGGAS CATGAGACAATACATATATAGGGGGGAATATATGGAAATTGAAA AAAAAAAGATGTGAAAAATAATAAATCTCAATAGAAAATGAAGGAAGCATAAATGAAATAAAAGTG AAATCAGGTGATGAGATAAAAAACAATTGTS TAATAATGCATCAAAATTTGTATATTTTTAAATATTA AAAGACTTTTTTATAAGTTATAAAAAATTATAATTGAATAYCACMAAATTTTATTATTTTTCTTAAAA AATCTTAWATGTTTTAATTGAATACCATAAGACTTTTTTATATAAAAAHTATTTTAAAATCTTTTMAA Gm08:827 8278001 79 262 0.884 0.741ATCTTAATCYAATATATCCACTAAGTTAT[C/T]AA 8001AGGCTAGGAGGAAACAAGTGGASCATGAGACAA TACATATATAGGGGGGAATATATGGAAATTGAAAAAAAAAAGATGTGAAAAATAATAAATCTCAAT AGAAAATGAAGGAAGCATAAATGAAATAAAAGTGAAATCAGGTGATGAGATAAAAAACAATTGTS TA AAAAAATTGACGATAAGTCTATAATAAATAAATTMAAATCTTAATCYAATATATCCACTAAGTTAT YAAAGGCTAGGAGGAAACAAGTGGASCATGAGACAATACATATATAGGGGGGAATATATGGAAATT GAAAAAAAAAAGATGTGAAAAATAATAAATCTCAATAGAAAATGAAGGAAGCATAAATGAAATAAA AGTGAAATCAGGTGATGAGATAAAAAACAATTGGm08:827 8278167 [C/G] 80 263 0.861 0.847T[C/G]TAAAAAAATTGACGATAAGTCTATAATAA 8167ATAAAAAGTGAGGTCATATACATATTCCCGATTT CTATAAAAAAAAATGAATATTTGAAAATCAATTCATTTTCAATYTTTAAAAAATAAATAAAAAAGAAT TGAAGTTGTATATCAATCTATGGAGAATTAATTCAAAAAATGATTTATAGAAGTTAGCAATAGAAAA AT AAAAGATGTGAAAAATAATAAATCTCAATAGAAAATGAAGGAAGCATAAATGAAATAAAAGTGAAA TCAGGTGATGAGATAAAAAACAATTGTSTAAAAAAATTGACGATAAGTCTATAATAAATAAAAAGTG AGGTCATATACATATTC CC GATTTC TATAAAAAAGm08:827 8278274 [C/T] 81 264 0.831 0.628AAATGAATATTTGAAAATCAATTCATTTTCAAT+C 8274 /T+TTTAAAAAATAAATAAAAAAGAATTGAAGTTG TATATCAATCTATGGAGAATTAATTCAAAAAATGATTTATAGAAGTTAGCAATAGAAAAATACGTACT AACATTATAAGAAAGAGAAAATATTTTAAGAGATAAATAGCAAAATAATATTTATTTAAS TGAATGA GTATCTTAAACCATATATCAAAATTTACAACACTAAAAAAAAATGAATATTTGAAAATCAATTCATT TTCAATYTTTAAAAAATAAATAAAAAAGAATTGAAGTTGTATATCAATCTATGGAGAATTAATTCAAA AAATGATTTATAGAAGTTAGCAATAGAAAAATACGTACTAACATTATAAGAAAGAGAAAATATTTTA Gm08:827AGAGATAAATAGCAAAATAATATTTATTTAA+C/G 8434 8278434 [C/G] 82 265 0.8580.647 + TGAATGAGTATCTTAAACCATATATCAAAATTTACAACACATTAAAATGAAAAATCTTAAAAAGAAG GAACAACAAAACTTTTTATGAAAATTATAACCAAAAAAAAATAAAAATTAATATAAAGCTTAACATTT CTTTTGTTGAAGTACTAATATAAAGCTTAACATGATAGCTAGGATAAGCACTATCC TATGGC CAC TTTTGGTAAACAGATTTAATTTGATGTAAATCATATTAACATAATTAATATTAGGTATTTTAATAATTT TTTATTATTTTATTTGTATTGTTCATTAWTTGTTRAATAATATATAAGATAAAAAACATTTTGTCATTT ATCTTTATCCTATCTTATTTTTTATCTTGTCTAATAGm08:827 8279165 83 266 0.83 0.759 TCATATTTTTAACAAATCAAATWGGG[G/T] GTAA9165 GTGTTTGATAAATTTTTTCAAACAAATTACAAATGTTAATATATTTTATTTTTTCAACAAKTAATATGT TAATCTTAATAAACAAATTCACATTTTATTTTTCATTTACCAAAATAGATATATTATTTTTAAATATTGT TTGAAATAAATAATTTATAATTAATTWAAAAAAATAAWAATTTCATTTCGTAACATA ATTTTTTATTATTTTATTTGTATTGTTCATTAWTTGTTRAATAATATATAAGATAAAAAACATTTTGTC ATTTATCTTTATCCTATCTTATTTTTTATCTTGTCTAATATCATATTTTTAACAAATCAAATWGGGKGTA AGTGTTTGATAAATTTTTTCAAACAAATTACAAAGm08:827 8279230 84 267 0.903 0.797 TGTTAATATATTTTATTTTTTCAACAA [G/T]TAATA 9230 TGTTAATCTTAATAAACAAATTCACATTTTATTTTTCATTTACCAAAATAGATATATTATTTTTAAATAT TGTTTGAAATAAATAATTTATAATTAATTWAAAAAAATAAWAATTTCATTTCGTAACATATTTTTCAC ATTGAAATAAACATGTACGACACACATATATACATACATATATATATATATATATAT AAAAATAATTCATATTAATATACCAACTTAAGAAAGCTGTTAAATATATTAAAAAAAGGAAATATGTT ATTATTAAATCAAATTTTCATCAGTTAACAACCAACATTTTAATCTAATTTAGTTGTTTAAACAAAATT TGTATGTATTATAAATTTTTAATATTATTTTTATTGm08:827 TTTAAAAATAAAAAACAGTGAAAACAAT [A/C] AA 9854 8279854 [A/C] 85 2680.842 0.759 CC TTGCATTATCATATATAGTCAATTAAAAAAAAGGAATGAGTGAAGGGGAAAAAGTGGAGGAAAA GGTAATGGATTCAATTCCTTCCATTAATATTTTAAACAAAAATTAATAAATTAACATATTGGTAAAAA ATATAATATTAATTTCTTGAAAATTTGTATCCAGTAGTACAACATTATAAATTATTTTTTAGGT TTCTGCCAATGGAAGGGTATCCAATGCGATTCATCCAGCCACGTGACCAGCATAAGCCTCGCTTCGCA KTCCCTCACCGGAACACTCCCCTCGGATCTCAATTCCCTCTCTCAACTCCGCACTCTCTCCCTCCAAGA CAATTCCCTCACCGGCACCCTCCCTTCTCTCTCCAGm08:828 8280901 [A/C] 86 269 0.929 0.848ACCTTTCTTTCCTCCAAACCGTCTAC TT [A/C] AAC 0901CGCAACAACTTCTCCTCCGTGTCCCCCACCGCYT TCGCCTCCCTAACCTCCCTCCAAACCCTCAGCCTCGGCTCCAACCCTGCTCTCCAACCCTGGTCCTTCCC CACCGACCTCACTTCCTCCTCTAACCTAATCGACCTCGACCTCGCCACCGTATCCCTCACCGGTCCC TT GCCGGACATTTTCGACAAATTCCCAGCCACGTGACCAGCATAAGCCTCGCTTCGCAKT CCCTCACCGGAACACTCCCCTCGGATCTCAATTCCC TCTC TCAACTCCGCAC TCTC TCCCTCCAAGACAATTCCCTCACCGGCACCCTCCCTTCTCTCTCCAAC CTTTCTTTCCTCCAAACCGTCTACTTMAACCGCAGm08:828 8280937 87 270 1 0.848 ACAACTTCTCCTCCGTGTCCCCCACCGC [C/T] TTC0937 GCCTCCCTAACCTCCCTCCAAACCCTCAGCCTCGGC TCCAACCC TGCTC TCCAACCC TGGTCC TTCCCCACCGACCTCACTTCCTCCTCTAACCTAATCGACCT CGACCTCGCCACCGTATCCCTCACCGGTCCCTTGCCGGACATTTTCGACAAATTCCCTTCCCTTCAAC ACCTTCGCCTCTCTTACAACAACCTGTTCCCGCTTCATTGACAAGTCTTCCTAGTTTGAA GAAAGTTTCTCTGGATAATAATGAGCTTCAGGGGCC TGTGCCCGTGTTTGGGAAAGGTGTGAATGTTA CTCTCGATGGGATTAATAGTTTTTGTCTTGATACTCC TGGGAATTGTGATCCCAGGGTGATGGTTTTGC Gm08:828 8281564 [A/G] 88 271 0.9240.824 TGCAGATTGCCGAGGCATTCGGGTATCC [A/G] ATT 1564CGGTYGGCAGAGTCGTGGAAGGGGAATGATCCG TGTGATGGTTGGAACTATGTTGTGTGTGCTGCCGGAAAGATTATTACTGTCAATTTCGAGAAACAGGG TTTGCAGGGTACCATCTCCCCTGCATTTGCCAATTTGACTGACTTGAGGACTTTGTTTCTCAATGGCAA TAATTTGATCGGTTCTATACCTGATAGAAGGTTGCTGATTTTGGGTTGGTTAAAAATGCAC CAGATGGGAAGTATTCTGTTGAGACACGGTTGGCTGGAACATTTGGATATCTTGCACCTGAGTATGCA GGTACAGAAAGCCTTTGATTTTAGTTTTGTACAATTGTGCCTTAATTTTGAAGTTCATATTTTATATGC Gm08:828 8282902 89 272 1 0.848TCGTATTTGGTGGTTATAGCTGTTGGTTA[G/T] TA 2902CTTCAATATCATGCTTCGGTGTTCAGCAAATTTA AGTAGTTCACCAGAGTAATCGCTCACATACAAAAAAAAAGTAGAAAGAGTTGAAGGGAAAATAATTG ATACTCAATTCCTAGATACATGGCTACTTCAAAATTCTTTGTGGCTATTTCTTTGCAATGTTATATTTT GC TC TTTTCACGTGTTTTGTTGAGTTGGGGAGCAATGGAAACCTACTAGCCATGATGAAGA AGAGGAAGACGGCTCTGGCGGTGACCTTCATATGAGCCTTCCTCAAGCTCTACGAAGGTGGCAAGCCA ACGAAGGCACTTCCTCAATATTTAATGACATTTCCATCTCACAAACCCAATCAAGCATCTCCTCTAAA Gm08:828 8284027 90 273 0.863 0.744CC TGCAGGGTTTGCAGAC TCC TTTGATTCAA [C/T] 4027GGATTGCCGTTAACCGAATTGATAAACGAGACA AC TATCCAAGGGCATCTTAGTCCATATGATAGTGGAAGGTTTAGTTGAGAATACCCAAGAAAACCAG AGGTTGTAAAGCTGTTTTGATCTATTAGCATCGCCAATTTCTTTGTAATTATTTATTATTGTTCAAAAT GTCATTTTTATGGTGTTCTTAAAATCTCCTCCAAGATTTGTAAGAGAAAAC TTC TTGGCTC TATA TTTAASAACAAAAAATCTAAGAKRAAATGGGATTKAATGGAAATGATCGGTCGCAAGCATATCTAAAT TTGACAGGAAATCCATAAATGAC TTGACCAC CATTAACAAGATAAATATTGTGTGAGATCTTTAAAAR Gm08:828 8286864 [A/T] 91 274 1 0.687TGAAGATTTTAC GGGTTTAACAGATTAAAA [A/T] C 6864TTTTACAATTTAATATCACATTCTTTTGAACACAT GAACACTTATTGATGATAGTTACATTCCATGCTTGC TTTCC TTGCAC TTTATTTTTTGTTGGAAATTGATCTAYGGAGAGATC TTTCAAGGAACATTGGC TAT AGCTGACATGATGATWGRAGGAAAAATTACAAACAATAATTTATACAAATTTTATGTTTCA TAMAATAGAAGAAACCAGTATCTTGACTTCTTGAGAAATGAGGACAAGGAGCAAAACTATGCTAAGA ATCTTGATGGCTGAACCASCCATTTCAGAAAATGTAAATACAAGCTTCGATTCTCGAATTGCATAGCT CTTATATGTCGCGTTATTTATAAATGAATTGTTGTGm08:828 AATTTGTAAAACAATATGTTTTACGTTTCG[C/T] G 7265 8287265 92 275 0.7760.917 TGAAGAATATCRCATTTATGAATGACTGAATTTTTAAGACAATGAAACTGAAGTTAAAGAAACATAA ATTACTCTAAAAAAAATTAAATACAGTGAAATTGTATAGATTTGATAAATATTTTTTTAATAGTTGATA TGATTTTGTTTTGTTAGGAGAAAGCTATCATTTTGTTCTCCTATAGTTATS TTTAGYAAGTTA AC CAGTATCTTGACTTCTTGAGAAATGAGGACAAGGAGCAAAACTATGCTAAGAATCTTGATGGCTGA AC CAS C CATTTCAGAAAATGTAAATACAAGCTTCGATTCTCGAATTGCATAGCTCTTATATGTCGCGTT ATTTATAAATGAATTGTTGTAATTTGTAAAACAAGm08:828 8287278 [A/G] 93 276 0.76 0.91TATGTTTTACGTTTCGYGTGAAGAATATC [A/G] CA 7278TTTATGAATGACTGAATTTTTAAGACAATGAAAC TGAAGTTAAAGAAACATAAATTACTCTAAAAAAAATTAAATACAGTGAAATTGTATAGATTTGATAA ATATTTTTTTAATAGTTGATATGATTTTGTTTTGTTAGGAGAAAGCTATCATTTTGTTCTCCTATAGTT ATS TTTAGYAAGTTATTTTAATTAAATTTTTTACGTTTCGYGTGAAGAATATCRCATTTATG AATGACTGAATTTTTAAGACAATGAAACTGAAGTTAAAGAAACATAAATTACTCTAAAAAAAATTAA ATACAGTGAAATTGTATAGATTTGATAAATATTTTTTTAATAGTTGATATGATTTTGTTTTGTTAGGAG Gm08:828 8287453 [G/C] 94 277 10.738 AAAGCTATCATTTTGTTCTCCTATAGTTAT[C/G]TT 7453TAGYAAGTTATTTTAATTAAATTTTTTTATTAATT AAAAGATTTATTTGACTATTTGATAAATAATTTTTTTAAGTAATTTTTAATGTTTCTCTAGTATYTTTTA GTATTTTTTTAAAATATTATTTAAAATAACATTTTTTAAACACTAATTTTTAATTTTTAACCTTTTAATT TTATTCTCTTTATATCTTAAAATGTTTCGYGTGAAGAATATCRCATTTATGAATGAC TGAATTTTTAAGACAATGAAACTGAAGTTAAAGAAACATAAATTACTCTAAAAAAAATTAAATACAGT GAAATTGTATAGATTTGATAAATATTTTTTTAATAGTTGATATGATTTTGTTTTGTTAGGAGAAAGC TA Gm08:828 8287459 95 278 1 0.591TCATTTTGTTCTCCTATAGTTATSTTTAG[C/T]AAG 7459TTATTTTAATTAAATTTTTTTATTAATTAAAAGAT TTATTTGACTATTTGATAAATAATTTTTTTAAGTAATTTTTAATGTTTCTCTAGTATYTTTTAGTATTTTT TTAAAATATTATTTAAAATAACATTTTTTAAACACTAATTTTTAATTTTTAACCTTTTAATTTTATTCTC TTTATATCTTAAAATATTTATTAACTTTTCAGTTTACTTTTGCAAATAAYATATTT CTTTCCTGGMATATKACAAAGCTAAACAATATTTCTTGAGTGTTTAATTGTTTTAAATTGAAATAGGA AGTGAGCATTTMCTAATATCTTAGCTCGAAACATCTCTTTCATCTTTGTTGAAGTAAACCTCTGTATGG Gm08:828 8288039 [G/C] 96 279 0.8840.584 TAAAATTAAGAGGAGAAAGAAAAATGAA[C/G]T 8039GGAGTAAGGTCTTGTTTGAAATTATTTTTTAATTT CAAAACTTGTTTTCAATATAATTTTTAGCTTTGTTATATTTTAAAAATAAAATAAAAAGAAAAAAYAT TTGTTAAAATTCAAAAATAGATTTTTTTTAAAAAAATGTTCATAAAATATCAGCATYTGTCAATTGCA TGTTTATGAGGTAAAAAATTGCTTTATTAAGTGAGCATTTMCTAATATCTTAGCTCGAAACA TCTCTTTCATCTTTGTTGAAGTAAACCTCTGTATGGTAAAATTAAGAGGAGAAAGAAAAATGAAS TGG AGTAAGGTCTTGTTTGAAATTATTTTTTAATTTCAAAACTTGTTTTCAATATAATTTTTAGCTTTGTTAT Gm08:828ATTTTAAAAATAAAATAAAAAGAAAAAA [C/T] AT 8141 8288141 97 280 0.823 0.713TTGTTAAAATTCAAAAATAGATTTTTTTTAAAAA AATGTTCATAAAATATCAGCATYTGTCAATTGCATGTTTATGAGGTAAAAAATTGCTTTATTTATGAA AATATTTAGGATCCAAAACAAGAGTAGGAAAGTAATTTTTAAAAGACATTTTTTTCCAGCACTGCAAT TGTAGGAACAAGTTTTAAAATACAAATGCC TCTGTATGGTAAAATTAAGAGGAGAAAGAAA AATGAAS TGGAGTAAGGTCTTGTTTGAAATTATTTTTTAATTTCAAAACTTGTTTTCAATATAATTTTT AGCTTTGTTATATTTTAAAAATAAAATAAAAAGAAAAAAYATTTGTTAAAATTCAAAAATAGATTTTT Gm08:828 8288200 [C/T] 98 281 0.8830.851 TTTAAAAAAATGTTCATAAAATATCAGCAT[C/T] T 8200GTCAATTGCATGTTTATGAGGTAAAAAATTGC TT TATTTATGAAAATATTTAGGATCCAAAACAAGAGTAGGAAAGTAATTTTTAAAAGACATTTTTTTCCA GCACTGCAATTGTAGGAACAAGTTTTAAAATACAAATGYCTTGAAAATCTTTCTAATACTTAATGGAA AATATTAAATAAAAATAAAAATAAAAATATAGGAAAGTAATTTTTAAAAGACATTTTTTTCCA GCACTGCAATTGTAGGAACAAGTTTTAAAATACAAATGYCTTGAAAATCTTTCTAATACTTAATGGAA AATATTAAATAAAAATAAAAATAAAAATAAAAATATTTAATGTTTTAAAAACTTTAAAAACATTCAA Gm08:828 8288470 [A/T] 99 282 0.8520.652 ATACTTTC TTTATTTAATAAGAGGAGGATGA [A/T] 8470GGGATTAGAATTATTCAATTTTTTTATATTAAAAT ATAACGAATCCATAACAAATTTACAGTAGTACTTTGTTTCATAAAAAAATACTGATTGGATGAAGCAG AKAGGAGAGAGGAAGATGTCAGTAAGTCATAAATGTGCCATTAATACATTTAATAACTTTTTTTTTTT ACAAAAGGGAGAAAGGCTTACATTTAAATTTTTTTTTTTTACAAAAGGGAGAAAGGCTTACAT TTAAATTGCTATTACTTTTTTTAAACGAAAAAGGGGTGAAAC GC CCAAAATAAATCATCATAAATAA GATAATAAGATAAGGAAGGAGAAAATAAATTTAAATATTGATCACAAATAAATTTTGYATAAATACA Gm08:828 8288831 100 283 0.852 0.612AATAAAATATAAGATAATAAATATCGATCAAT+C/ 8831T+CGTGAAACAATTTGCGGAAGAGCAAAATTTGA GAAAAAAAATCGAAGAARCAAAATTCGCGATATTATAAAACTTTAGAGATAAAAAAAAATTCATGAT AAATAATACAGTATATTATAATTTTAATCTTTAGTTTTTAATACAACTGTAAAAAAAATTCATGATAAA TAATATATTATAATTATAATCTTTAGTTTTAAAACTTTTTGTTAGTAACAGAAAGTGTAAACTGGT TTGGAGAAAATGTGAGAGATGGCAGGATACTATGAGTAACTAGTTGGATTGGAAAATGTTGTATCCA GCTGTAAATTACCCATTCCATTATTGGAAGGAAATATTCCGCATGAGCCAAACTATGCGAAAATGACA Gm08:828TGGTGAAAATTGATAAAGGTAAAGAAAAAGT+A/ 9392 8289392 [G/A] 101 284 0.9290.785 G+GAGCTCAGAAAGGTGTTATTCTTCATCAAGAAGAGCTATTTCCAAAGCAACTATRTTACTTGTGCA ACTCTTTATTTTTTGTACATATACTACTATTATTATTACTTGTGCTACTCTGATAAATAGAAAGTAGAA AACAAAGAAGTGGTATTGATTGATGTTACGTAAGTTACATAAAAGTTTGATGCGTATTGATTGAT ACAAAGCAATGGATCCAGGACTCATATATGATATCACCACTGAGGATTATGTCCAATTCCTATGTTCC ATGGATCACAGTAGTGCATCCATTAGCAAAGTGACTAAGACCACCACAAGTTGTAAGAAAGGAAATC ACCAAGCACTGAACCTCAACCTTCCTTCCATATCGm08:829 AGTGCCAAACCTGAAGAGGGCTGCAACAGTA+A/ 0740 8290740 [A/T] 102 285 10.912 T+TGAGAACAGTGACAAACGTGGGAAATATTACTGCAGTCTRCAAAGCTCTAGTGAAAGTTCCACATG GCATAAAAGTTAGAGTTGAACCTCAAACTTTGAGTTTCAATTCAGRTGTACGAATCCTTAACTTTAKTG TCAGTTTTCTGTCAACTMAAAAATTTCATGGAGATTACAAATTTGGGAGCCTAACATGGACAGAT TAATATTTTTTCTTTTTAAAATACAGAWGGAAGTACAAGAATAAAAAGTGGTTCAACTTCCATGAATA AAAATGGTCTTTACATGATTTGCACTTAATCTAAATAACCAAGCACAAAATATATCAAAYWTGTGTA TATTTTCAGTTTAGTATTAATTATTAATGACTAGCGm08:829 8291682 [G/A] 103 286 0.866 0.715AATAGAATTTAGATTTATAGAGACAATACA[A/G] 1682TTAGTAAATTTTATTTTAGAAATTATTTTAAAATA TTCTAATAATTAAATTACTCTTTTGTTTTTACATTGCAAGTGCAAGCATCTAYGTGCAAAAGGAGGGT ACGATACTCAACAATAGATAAATTTGCACAACATCATCAGTCTTTGTTYTTCTTTTTCTTTTTTACTTTA GATACGTAAGGCAGTAACAACATACGAGACAAAAGATAAGAGAAACAAGCTTACATTACT ACAACGTTATAAGAAGCAAATAACCTACGAAGAAAATCAAGATAAATAAATAGATGGTACAAATTT GCATGTGTTCGGATATCCATCGACATCATTCATTTCGATCAAAATTCACGTTTTGGACATAAAAGCAAT Gm08:829TCTTCGTCGCTTCAGATAATGCGTGTCGTGGA+A/ 2207 8292207 [G/A] 104 287 0.9120.904 G+CAGAGGATGCAAAACCATACATGCAGAAAATTATGCTTGCAGAATGACACWTACGATGGAGCACC AAGATATGAGGCAAGTCGTAAAATATCACTAAATATTCCACCAGCGGTGACTTGAGCACCAGCTCCT GGCCCACGAACTATCAGAGGCTGATCCTTATACCTTCGTGTTGTAAATGCAATAATGTTATCTGACCC CTGTTATTGATTGATSAATCACTTATTACTATCTGATGGAAGATGAGTTTTATATAATAGAGTTACCTT GTCCTGCAAGCTTACAATAGAAAMTTCAGCTGYCTACAGCTATTAAGACTAACTAAACTTCAGTTAAG CCAATATTAATTGTGTTTTACTATTTAAGTCCTAGGm08:829 8297064 [C/T] 105 288 0.929 0.857TTTACAATTTCTCCTATATTTTTATTTC[C/T]ATTA 7064CTTGTTTCGAAAGCAATCATCTGAATTTTCTCTAT CTTCTTGTATAATGATAAGAACCTTGGGAGATCTACACCACAAAAACTAGTCATTGTAGTTTGGAGAG CCAAGGACCTTATACATCCTAAACTTCAAATGTGAGACTCAAGTCTCATACCTTGCAATTGGATCCTA ACATTCCATCTTGCTTTGCAGCCACAAATGTAGAATGATAAATCTTCAGTCTGATATCA CTAAAGAGAGTCAAGTCTTAACAATTGAACAGAAACATGCATTTGGTTTTAGAAGAATTGGATTTAGCACC TGAGAAAGAC GC CCATTATC CAAAGCTTGACGAAATC TAGATTGCAATGCC TCAGCAACAGC TT Gm08:829 8299433 [A/T] 106 2890.929 0.787 TTACTTCTTTCTCGGGCACAGCAAAGCATAC [A/T] 9433GAATGCTCACTACTAGCCTACATAAATACTGTTA ATGATTAATGCCATTTCTTATATATCARCGTGGACAACTAGAAAAATTGAAAAAAGTTATAAGTGCA CC TGAGATATCATGATAACATTAGCTC CAACATCTTTTACTGCACCAAAAATAGCACTGGCAGTACCT GGAACACCAGCCATTCCAGTTCTGCAAAAAATTAATGCCATTTCTTATATATCARCGTGGACAACT AGAAAAATTGAAAAAAGTTATAAGTGCACCTGAGATATCATGATAACATTAGCTCCAACATCTTTTA CTGCACCAAAAATAGCACTGGCAGTACCTGGAACACCAGCCATTCCAGTTCTGCAAAAAAGCATCAA Gm08:829 8299672 [A/T] 107 290 0.9190.702 AGAAAAATTTATTGGAATCTACAACTTGGAC +A/T 9672+ATTAATATTGGTTAAAGAAAACCTTAAATTAAATAGAAATC CTC GTGCAGCAAAAAATGC CAAC TATTCATCATGTAACACAACTGCAATTCATGACTCAC CCCTCGACGTTTACAAGTGCCAAGTTGTCTATGGTTGCAAATCCTTTGACAAAATTTTGCAGGTTCTG GC TATC TTCATGATCATTAACAGAAGGATGGCTTGTGGATAAGGTCATACATCATATCTGTCACC TTTGACATTGCAGAAACAACCACCAATTTCCTCTCC GAATCATCC TTAAGAATTATGTC YGCAACATTTTTTATTCTC TGAGAGGTTCC CACACAGGTTC CACCAAATTTGTGAACAGACCAAGTTTCTCCTTTGGG Gm08:830 8301839 +GIN 108 291 0.9370.721 TAGTTGTTTTTCCTCCAAGGACACATTCG[A/G] TG 1839AAACATCTGCTAGCAAATATAGAAAGGACAAAA AAACATAAGTTACTGTATTTGTCTATTAGAGTTCTAAGGTTGACTTGATGGTAAAAGGAGAAGGGAGA GAGGGAAAGGTCGTGGGTGGGTTCAATTTTCTCCGC TAACAAAAAAC TAACAATTAACAAC TAATATT TGCTGATAATAAAAAAAACTRTATTCGTCGAAGGGAGAGAGGGAAAGGTCGTGGGTGGGTTC AATTTTCTCCGCTAACAAAAAACTAACAATTAACAACTAATATTTGCTGATAATAAAAAAAACTRTAT TCGTCTATTTCAAAACATAACCATAAGAGTAAGTCGTAACCTGTAAATGAAGCACGTACAGATGTACT Gm08:830 8302134 [C/A] 109 292 0.9240.758 CGGTGCC TC TCTTC CC CGTGGTAAAGTAAGA [A/C] 2134CC TTCC TGAGACAGAAACCATTGTATC GTC GTGA ATCAGTATATAGCAAAACACAAAAATCCAATTAATCTCATGGGGAGAATATCATTTAAACTGCCAAA ATTCCGAAAACACTCTAATCTCTGCAAAGGATAAATATACAAAAAGGAAAAAAAAAAGTACAGAATA TACTGCTTGTAGAACAACCAATCATCTAAGAGTTGAGTTGAAATAATGAAATGAAATGGATCATAA TCCATCATCATCTTCCATTATGTTTCATTTCAACTTTTACAAATCAAACAATCCAACACCTTTTCCTTCCAC TCCATCC TTC TTCATTC CATACTC TACAACCAATCAAAACATATTCGAAGGTTTCCATGTATGTAGA Gm08:830 8303450 110 293 0.843 0.582ATTATAAATAGGTTGAACAAAATTTTA[C/T]TGRG 3450TAGGTTGAAMAGAATTATTTGGTAYTATTATTCG TACGCC CC TAAC CATGTGTTTGGATGAAGAATTTAAAAATTTCTAAGAAATTTAAATTCATAACATTT TAATTGCCTTGATTTTAATTCCTTTCCTTTTGTAAATATTTTGTTTGGATGAGGTAATTCAAATTCTTGT ATTTTAATTTTCTTS TTTGGACAAAATGATAACAAATTGTACATATTATAGACTAAAA TGACAATAATTTTAATCTAAACAATTTATTTATATTTTTTTAATTTTATGATGTGTTAAATTGTGACAGTGC CC TACAATTTTAAAGAAC GTACAAAATAATTATTTATTCAAAATTTTAAACATAACATTACCTTTCC Gm08:830 8305237 [A/G] 111 294 0.8170.722 CTACAAC GTCC CC CCGATAGTGTCATC [A/G] GTAG 5237GAC TC TTGC TTCAGAACAAAAC GC GAGTC CATATAAGGCAACTGCAATTTTTTTAATTAGTCTTCCGTT TGTTTCGGGGGCTAATGGGGAATTATAGCAAGTGTGAKAATTTTCTATGCTTTTAAACTAAAATCTAC ATATTTATAAAAATATAAAAGTAAAAAAAAAATGC CAC GGATAGTTCAGTCAAAGATAA AATTTTAAAGAACGTACAAAATAATTATTTATTCAAAATTTTAAACATAACATTACCTTTCCCTACAACGTCC CC CCGATAGTGTCATCRGTAGGAC TC TTG CTTCAGAACAAAACGCGAGTCCATATAAGGCAACTGCAATTTTTTTAATTAGTCTTCCGTTTGTTTCG Gm08:830 8305348 [G/T] 112 295 0.9190.737 GGGGC TAATGGGGAATTATAGCAAGTGTGA [G/T] 5348AATTTTCTATGCTTTTAAACTAAAATCTACATATT TATAAAAATATAAAAGTAAAAAAAAAATGCCACGGATAGTTCAGTCAAAGATAATTCGAAATCATAG TAAATATTAAATGATTGGATTTTACAACATS TATTTGAAAGAGTCATCATAAAACTTAATACCACAYTT TAACCMAAAACTTTAAAAGTCAACTTTATCCAATCCTATTATGTTACCCAAGATGYCGTWAGT TCTCTAGGTGGTTTTTTCRAAACAAAAAAAAWTTATTTGTAATAAAATAAATAATATTACTTCATTCTC ATGTCTTTTTATATTTAAGGTTATTATTAAGAAATATTTGATGAAAATAAACATTGTTCACCCTCGTAG Gm08:830 8305905 113 296 1 0.491CC TCC GTTATGGC GAGAGTGCC TCTCAT [C/T] TGC 5905GTTC CRAACAGC CC TAGC TTRCACCATAATGGGTTGTGTCACCCTCGTAGCCTTCCYTGCATTCTCATT ATCATAAACGAYGCCGCTTTGGGAGACGCCTTCCATGTC TATRCCAC CC TTCAGAGCATAGGC CC CACCATCTTGAGCTTGTGGGYTGTCGGACTAGGGYCG CTCTCTAAAGYCACCACCGCTGTAGCGAGAGTGCC TCTCATYTGCGTTC CRAACAGCC CTAGC TTRCACCATAATGGGTTGTGTCAC CC TCGTAGC CTTCC YTGCATTCTCATTATCATAAAC GAYGC CGCTTTGGGAGACGCCTTCCATGTCTATRCCACCCTTCAGAGCATAGGC CC CACCATCTTGAGCTTGT Gm08:830 8306090 114 297 1 0.494GGGYTGTC GGACTAGGGYC GC TC TCTAAAG[C/T] 6090CACCAC CGCTGTAGC GGTGGC GCTC GC CGC GTTTGTGGTGGTTCTTTCCTRGCCTCAGAGCACAAATT TGATAGCTAAACGCATATCATTGGGTCAGATAGTAC CACCATGTTGAAATTRAGAGGAAAGAAGTTTT AAAAAC CC TAATTTGAGGAAGAAGAAGCAAGTGAAGAAGAAAATATTTGACAACTTTTTAAAAT GTTGTGTCAC CC TCGTAGCC TTC C YTGCATTCTCATTATCATAAAC GAYGCC GC TTTGGGAGAC GC CTTCCATGTCTATRC CACC CTTCAGAGCATAGGC CC CAC CATC TTGAGC TTGTGGGYTGTC GGAC TAGGGYCGCTC TCTAAAGYCAC CACC GC TGTAGC GGTGGC Gm08:830 8306141 [G/A] 115 2980.848 0.737 GC TC GC CGC GTTTGTGGTGGTTC TTTC CT [A/G] GC 6141CTCAGAGCACAAATTTGATAGCTAAACGCATATC ATTGGGTCAGATAGTACCACCATGTTGAAATTRAGAGGAAAGAAGTTTTAAAAACCCTAATTTGAGG AAGAAGAAGCAAGTGAAGAAGAAAATATTTGACAACTTTTTAAAATTTGCATCAAAGTCCAGCTTAC ATGTCATAATCTAGGACAATTTGWCACGTTCCATGTCTATRCCACCCTTCAGAGCATAGGCCCC ACCATCTTGAGCTTGTGGGYTGTCGGACTAGGGYCGCTCTCTAAAGYCACCACCGCTGTAGCGGTGGC GCTCGCCGCGTTTGTGGTGGTTCTTTCCTRGCCTCAGAGCACAAATTTGATAGCTAAACGCATATCATT Gm08:830 8306210 [A/G] 116 299 0.9290.772 GGGTCAGATAGTACCACCATGTTGAAATT[A/G]A 6210GAGGAAAGAAGTTTTAAAAACCCTAATTTGAGG AAGAAGAAGCAAGTGAAGAAGAAAATATTTGACAACTTTTTAAAATTTGCATCAAAGTCCAGCTTAC ATGTCATAATCTAGGACAATTTGWCACGTTAGATAATCTATGTGACAYTAAAATTATTAAAAATATAT CTCATTAATGGYGTTAYTTTTAAATTTAACGTGCATCAAAGTCCAGCTTACATGTCATAATCTAG GACAATTTGWCACGTTAGATAATCTATGTGACAYTAAAATTATTAAAAATATATCTCATTAATGGYGT TAYTTTTAAATTTAACGGCAAAKACTATTTTRTAAAATTTATGCAAAAATAGAGACTATTTTTTACAT Gm08:830 8306492 [A/G] 117 300 0.8530.614 TTAAAAAAAGATAAAGACTAATTTGCAAAA[A/G] 6492GAATCAAAAGTTAGAAATCAAAATACCTATTTAY TTAAWAAAAAAAACATCATGCGTTAGTTATAACCTTAACTTCTAATTTTTTGCTAACGCCCAAAAAA ACTAAGAATTCGAATCAGAAGTAGGYAGAATAGKCAATTTGGTTCTTAAAAGTGTATGGAAGGAAAA AWTTTCCTTTGACTTTTTAAATTGGAACACGTAAAATTTATGCAAAAATAGAGACTATTTTTTACA TTTAAAAAAAGATAAAGACTAATTTGCAAAARGAATCAAAAGTTAGAAATCAAAATACCTATTTAYT TAAWAAAAAAAACATCATGCGTTAGTTATAACCTTAACTTCTAATTTTTTGCTAACGCCCAAAAAAA Gm08:830 8306627 [G/T] 118 301 0.8110.689 CTAAGAATTCGAATCAGAAGTAGGYAGAATAG+G 6627/T+CAATTTGGTTCTTAAAAGTGTATGGAAGGAAA AAWTTTCCTTTGACTTTTTAAATTGGAACACGTCTTGATTTTTTTCCCTTGTTGCCCAAAAGCAGTCTT ATTATTCATCCGTTGGGAATTTTTGTTTTAATTTCGCTGATMAAAAAATTGAGAATTTTATGTCTGCTT TGTGAATTACCATTTTWTCGGAACCTGCATTAGAAGKAATAATTTTGTTTTGGCTTGTTGAATT GGAAAATGTTACAGTCCCGGTCATTCTTTTTATTTTTATATGTTTATTTATTTTTGTCCAAATAGCAGGG TCATATTCAAAACTTGGGTTTTACTTTCAAGCTTTGGAACAATGTTAGTGTAATTTGTGACTTTTGATA Gm08:830 8307172 119 302 0.854 0.63AAGCCAAAGAAGTAACTTTCGTTCTTA[C/T]TTTC 7172ATGTGACTTGTAACAAGTTACAAGTCAGTAATAT AACCTATAACTTWYTCTTCATCRTCTGCTTCTTCTTTTGATCATAATATCTGTTAAGTGATCTTTCATAG AGAGAGAGAGAGAGAGATGGAGAGGTGTGACAAGGTGATGAACCAACGCAACATGCATGATTGTCC TAAAACAGGTCCTGGCTATCCTTCACTCTGAAAAGGCCAATTCAGCTTCATTGGAGGAAT AGATAGGCATTAGGCAGAGAGATCAAGATAGGTTTCTCAAGTTGTTGTTACAAACATTTTATATGACA TGATACTGGGAACAAGTGACATGTAGAAATATCTATCTCTTTCTAGTGCTATGCATGAAGACTTGGTG Gm08:830 8307665 [G/T] 120 303 0.9240.772 CAGCTTAAACAATTTCTGTCAAAACGTGTA[G/T]T 7665TTGGTGATTTTATATATATATATTGGTGATGAATA TTCAATTCAATGCAGGAACAGGAAGGGATAAGCCTGACTTTCTGGCCACAGTGGATGTGGATCCAAG CTCTCCAACGTATTCAAAAGTTATCCATAGGTTACCTGTACCTTATTTAGGTGATGAACTGCACCATTT TGGGTGGAATTCATGCAGCTCTTGCTATGTGATGAACTGCACCATTTTGGGTGGAATTCATG CAGCTCTTGCTATGGAGATCCATCAGCAGTTCGGCGATATCTGATTCTACCTTCACTGGTGTAAGATA CTAAACAGC CAC TTTGGATTTTACTTGCAC GCATATGCGCATGCAYACACACACATAACAAACACTG Gm08:830 8308019 [A/G] 121 304 1 0.837ACAAGGTTCAAGAACTTCACTGGTGTAAGAC +A/G 8019GATTTACCATATTTCAGATCAGGCCGCATTTATG TGGTTGACACAAGATCAAATCCAAGGTCTCCATCTTTGCACAAAGTTGTTGAGCCAGAAGACATCATA AGTAAGACTGGATTAGCTTATGCACACACATCTCATTGTCTTGCTTCTGGTGACGTCATGATCT CTGGTACCAACCACAGCATAAGACTATGATTAGCTCATCATGGGGTGCTCCTGCTGCTTTCACCAAAG GTTTTAACTTACAGCATGTCTCTGATGGTCTTTATGGGAGGCATCTACATGTATACAGCTGGCCTGGGG GTGAACTGAGACAAACATTGGACCTTGGTGAGTCGm08:830 8308891 122 305 0.936 0.801AGGGGTTC TACC CTTGGAGGTACATTGC T [C/T] AA 8891TAAATAATTCTGGAGTTATTTCCWCCAATTATAA GCACTTTATGTTAATGTACTTGTGATTTAATCATAAATATGTTTGTCCTTTGCTACATTTTTTCTCTCTA GC CTGTACTTGTGAAGTAATATGTTAAAGGTGGCATAATTTGTAAGCAACTTGTCCTAAATGCAGGTA AGGTTTCTGCATGATCCTTCTAAAGATGATTAGCTCATCATGGGGTGCTCCTGCTGCTTTC AC CAAAGGTTTTAACTTACAGCATGTC TCTGATGGTCTTTATGGGAGGCATCTACATGTATACAGCTG GC CTGGGGGTGAAC TGAGACAAACATTGGAC CTTGGTGAGTCAGGGGTTCTAC CC TTGGAGGTACATT Gm08:830 8308917 [A/T] 123 306 0.870.865 GC TYAATAAATAATTC TGGAGTTATTTCC [A/T] CC 8917AATTATAAGCACTTTATGTTAATGTACTTGTGATT TAATCATAAATATGTTTGTCCTTTGCTACATTTTTTCTCTCTAGCCTGTACTTGTGAAGTAATATGTTAA AGGTGGCATAATTTGTAAGCAACTTGTCCTAAATGCAGGTAAGGTTTCTGCATGATCCTTCTAAAGAT ACAGGTTTCGTKGGGTGTGCATTGTGTCAAGTAACATGGTAC GGTTTTTCAAGAC C GAG GATGAATCATGGAGTCATGAGGTACACAAAAAGGATATAGTAAAAAATCAATGCCTAAATTTTAGGA GAATCATGACATCTCATTAATCAGAAGGTTTACATTCAGCTATTCTATTTTTATTTCATTCCTATAATTT Gm08:830 8309316 124 307 0.9240.912 TGGGATTCC TGGTTC TTGGAATTTCC TTT [A/T] TA 9316ATTTTCTTCACCTTTTCTATATATTGTATCTGTGCT CATATGAAATAATAGAGATGATATAATTTTCATACTCTACTCTACTCATAGATATCCATACTCATTTTR TATTGTCATCTGGTATGCGTTTGTGCAGCTTCAACCAAGGTATAATGATCAATAATAC TTACACAC TAG AC TGAC TTTGCAGGTTGCAATATCTGACATCTCATTAATCAGAAGGTTTACATTCAGC TATTCTATTTTTATTTCATTCCTATAATTTTGGGATTCC TGGTTCTTGGAATTTC CTTTWTAATTTTC TTCACCTTTTCTATATATTGTATCTGTGCTCATATGA AATAATAGAGATGATATAATTTTCATAC TC TACTGm08:830 8309423 [G/A] 125 308 0.854 0.824CTAC TCATAGATATC CATAC TCATTTT [A/G] TATT 9423GTCATCTGGTATGCGTTTGTGCAGCTTCAACCAA GGTATAATGATCAATAATACTTACACACTAGACTGACTTTGCAGGTTGCAATATCAGTGAAACCATTG AAAGTGCAAAACTGGATTCTTCCAGAAATGCCTGGGCTTATAACTGATTTTCTGATATCTCTTGATGAT CGGTTTCTGTACTTTGTGAATTGGCTAGACAATATAACATTGAGGAC C CTAAAAATC CT GTACTGACTGGCCAAGTATGGGTTGGGGGACTACTTCAGAAAGGAAGCCCTATAGTAGCAATAACCG AAGATGGTAATACTTGGCAATCTGATGTTCCAGACATCCAGGTTTGTGCAGTTTAACTTTTGAAATTA Gm08:830GTGATTCTAGTGTCATGCTTGTTGATTTCTC [A/C] 8309837 [A/C] 126 309 0.924 0.8249837 CATGTTTGGAGTTGATTGGTTCTTAGATGTACTAGATATAATAGACTTGTGCATTACATTGGTGCCTT CAAACTTTTTGTCACTTTTGTATTTTATCTTGTGTTATGCTTAAACGTGGTAAATAATTGCACTTTAAAT TTTGAC CC TTTAGTGGTTGAAGGTGAAGAGATCAAAATTTTTAATTTCAGGGAAATAAGTTG AAAATGGTGGTC TGAAAATTAAC CCTAATTTC TTTGTTGAC TTTGGAGC TGAGCC TGGGGGTC CC TGCCTTGCCCATGAGATGAGATATCCTGGTGGTGACT GCACTTCAGATATATGGATTTAATAGC TATGC TACTTGAGGCCAGGCTACAAGCAATATCCATGTGAA Gm08:831TAAAATCCTTAGTCCTAGAATGAATCGAGG[A/T] 8310383 [A/T] 127 310 0.918 0.6770383 GGGCTAATGTTATAAATAAATAATAGTTGCATATGTATGATGGTTGCATTGTAATAAAGTTATATTGT CATGTAGTTTTCMGTACTTTCTCATTTACATCATCCTAAACAGTGTTCTCTRTGAAATAAATCTTGCTC AC CTACAAAATTTGGGTC TTC TGATTGAGTAAATCTCTATTGGAGTAACATTCTAGATTAATG TGAGATATCCTGGTGGTGACTGCACTTCAGATATATGGATTTAATAGCTATGCTACTTGAGGCCAGGC TACAAGCAATATCCATGTGAATAAAATCCTTAGTCC TAGAATGAATC GAGGWGGGC TAATGTTATAA ATAAATAATAGTTGCATATGTATGATGGTTGCATGm08:831 8310464 [A/C] 128 311 0.924 0.787TGTAATAAAGTTATATTGTCATGTAGTTTTC [A/C] 0464GTACTTTCTCATTTACATCATCCTAAACAGTGTTC TCTRTGAAATAAATCTTGCTCACCTACAAAATTTGGGTCTTCTGATTGAGTAAATCTCTATTGGAGTA ACATTCTAGATTAATGGCCTTACTTGGGATTCTATGATTTTCATTCACATCATGAATGTGCTGCACCTTC TACGTTGCTTGTTCCCATTTGAATGYATTTAATAGCTATGCTACTTGAGGCCAGGCTACAA GCAATATCCATGTGAATAAAATCC TTAGTCC TAGAATGAATCGAGGWGGGCTAATGTTATAAATAAA TAATAGTTGCATATGTATGATGGTTGCATTGTAATAAAGTTATATTGTCATGTAGTTTTCMGTACTTTC Gm08:831TCATTTACATCATC CTAAACAGTGTTC TCT [A/G] T 8310503 [A/G] 129 312 0.9330.734 0503 GAAATAAATCTTGCTCACCTACAAAATTTGGGTCTTCTGATTGAGTAAATCTCTATTGGAGTAACATT CTAGATTAATGGCCTTACTTGGGATTCTATGATTTTCATTCACATCATGAATGTGC TGCAC CTTC TAC GTTGCTTGTTCCCATTTGAATGYATTTGAAATCACA AC CCAAC CAAATCATTTCAATATGATGCMGTACTTTCTCATTTACATCATCCTAAACAGTG TTCTCTRTGAAATAAATCTTGCTCACCTACAAAATTTGGGTCTTCTGATTGAGTAAATCTCTATTGGAG TAACATTCTAGATTAATGGCCTTACTTGGGATTCTATGATTTTCATTCACATCATGAATGTGC TGCAC CT Gm08:831TCTACGTTGCTTGTTCCCATTTGAATG[C/T]ATTTG 8310663 130 313 1 0.847 0663AAATCACAACCCAACCAAATCATTTCAATATGAT GTACTTCTTAACAAATCAATGCACAAATAATTTTAATCATAAATTCAGAACTTATGCAGTGAATATTC TCGTTGTTAAGTTATAAGGGGC GGGGGGAATC TTATATATGTGATTTTTGGTATATGAACGTTTGGTTT GTGAATTGTGATTGTCAGATGGTAACAACAGAGGATGCTCCAGGATATGCAAATGCA GAAAATGAAGTCTTCAGTTCGTTCAATGGGAAGAATAAGGAAATCATATACCTATTTTTCATCTTTTAT ATTTATGCAGTCGTCTATGATGAATTGATGAGTGTTTTCCTGGCCATGTGTGTTGTTTTGGCTTCTGCT Gm08:831TTGTAAACACAAGATAATAATACAGGCAC [A/C] A 8311631 [A/C] 131 314 0.843 0.7721631 TAATAAACTGTATAATGACATGAAGATCAATATCTTTCTTTGAAGCTAAGAAAAATTGTTATAGCATG TAGCTACTTTTGTTGTCCCACAAATGTGTGGCATGGAGCAATTTTTTAATATATTCAAAATATTTATTT TGTGGACTCGACAGTCTACATCTATTTTATGAAGTGTAGTGAATCCAACATCAAACCCCTTT AC TTTTGTTGTC CCACAAATGTGTGGCATGGAGCAATTTTTTAATATATTCAAAATATTTATTTTGTGGAC TC GACAGTC TACATC TATTTTATGAAGTGTAGTGAATC CAACATCAAACC CC TTTGTCC CACTTTACAAAAACCCTCTGATCATTTGAACCTCCTAAATG Gm08:831AATACAAAC TGTGTCCATAAAAAAAAATT [A/G] T 8311906 [A/G] 132 315 0.824 0.621906 TGTGTCCTACGTGCTT CACTAC CC TATTTTGTTTTTATCATGTTAAATATATGAAAATAAATTATTGCCAAGTCCAAATTGTTTG CTACTATTGAAGCCTGCATTTGTCTCGATGTAAAATAGTAGTACTTATCCAAACACAGTATCAGGTTG AAGCAAACTAGTTCATATTATTGATGAGACCACCACAACTGTATGTTGAGGTCCATTGTCTGA TAGAAGACTGAGAGTTTAGGTGGGGCAACTTCGAGGAATATGTACCAAATATTTTAGATGTATGATT ATATCAACACACACACCTTTGCCTCTGTTCTCTCCTTTTTC TTTTGCCATGATAATAC CC TTCC TATAAT Gm08:831 8312536 133 316 0.9240.824 CC TATTCAC CCAAC GC CACATTTGTTTTC [A/T] TG 2536TATACTTAAATGTGTGTTAAGGGTAAGGGCTTCA AATAAGAAACTTAGCTAAAACAGTTAAGTAACTATTTACTCCCATCATTTTGCACAAATTTTTATGAA CTTAGATTTTACCAAAGGAGGGACAAAACTAAGAAC CAAAAAAWTATCATCATATTCAGAWGC CAC AACCAACCACATGTTTTCTATACATATTTTATTTTGCACAAATTTTTATGAACTTAGATTTTACC AAAGGAGGGACAAAACTAAGAACCAAAAAAWTATCATCATATTCAGAWGCCACAACCAACCACAT GTTTTCTATACATATTTTTTCAATATGGGGTACTAACAAAAAAGTCTTATTTGGTATGGAATTTTTAAT Gm08:831TACTCTATATTTATAGTATACAATATACTTG[A/G] 8312819+ G/A+ 134 317 0.87 0.8362819 GACATATTAGAATTTTATCTTCCAAGAGCAACCTAATCTCAGTTATC TCATACATATGCAATC GC TTAT TAGCAGAGTAAATCAGWAGTCTTCACAGAAAAGAGAAAAAAAATCATCTGTAGCACATGGAAAATA ACATAATTTCCTTGTTGTCCAAAAGGTTTGGTGAAGTGC GC TCTATCAGC TTATCAC TAATGCAA GC TTC TTAGTGGAGAGTGGAAGRWAGGGTACATCCAATCCAAGACACAGAACAGAAGAATGGCCTC AAAATCATCCACCATYARACTTGTTTGTTTCTGCTAC TTCATGC TCTTCAGC TCTATGCATTTCAC CAGCTGCACCGTGCTCTCATTGAAAAGTCATGCAAGCA Gm08:831CATGCAATGGTTCCATAGCTGAATGCAATC [A/G] 8313273 [A/G] 135 318 0.854 09 3273AGAAGATGAGCTGTTGATGGAGTCTGAAATAAG CC GAAGGTTTC TGGAGCAGAAGAGATCATACATTTCCAATGGAGCTTTACAGAGAGACAAACCAGTTT GTAATGGTGGTGGCTCTGGTGAAGCTTATAGTAAAACTGGAGGGTGTCTTCCTCCCCCCTCAAATCCT CAAAGTAGAGGCTGCTCTAAGTATTATCGTTAGGAAAGATCTATGATTGTATTAATTATCCGTTT CTTGTCATCTCCAATCTTTCTTTGTTCCATTATGCTRGATGGAATTTGATTTTTTCTTCTTTTTTTTTTGG GTGAAATGTTTTKGTAATGCACATAATGCAAC CATAAGGTATAAATC CTC TTACACATTCTAC CTC GA Gm08:831TATACATATTTAAATAATAAAATATAT [A/G] AAA 8313923 [A/G] 136 319 0.655 0.8063923 ATATAGAATTATATAAAATGAGATTTTATTTTAAACATATAAGAGTTCACRTGGGTAAAGTATTCACA TTCAC TTTACTATTAYCAAATAAAATTTGTS AGAAACATTTTCGGCTCAACATCATGCAATTAAACCA GAAACTTATGTCTCAATGTCAYATTCTATYAGATCATTTTATTCYGACATCCTCCAACATA TTCTTCTTTTTTTTTTGGGTGAAATGTTTTKGTAATGCACATAATGCAACCATAAGGTATAAATCCTCT TACACATTCTACCTCGATATACATATTTAAATAATAAAATATATRAAAATATAGAATTATATAAAATG AGATTTTATTTTAAACATATAAGAGTTCACRTGGGm08:831 GTAAAGTATTCACATTCACTTTACTATTA[C/T] CA 8314010 137 320 0.8420.823 4010 AATAAAATTTGTSAGAAACATTTTCGGCTCAACATCATGCAATTAAACCAGAAACTTATGTCTCAATG TCAYATTCTATYAGATCATTTTATTCYGACATC CTCCAACATAAGATTTCTTAAAGCAATCCATCTAGT CATTTGCTTCCACAAACACAAGGTTCGAGATCATCACAAGATCCAAACACAAACAGCAYAC TGGGTGAAATGTTTTKGTAATGCACATAATGCAACCATAAGGTATAAATCCTCTTACACATTCTACCT CGATATACATATTTAAATAATAAAATATATRAAAATATAGAATTATATAAAATGAGATTTTATTTTAA ACATATAAGAGTTCACRTGGGTAAAGTATTCACAGm08:831 8314025 [C/G] 138 321 0.817 0.808TTCACTTTACTATTAYCAAATAAAATTTGT[C/G]A 4025GAAACATTTTCGGCTCAACATCATGCAATTAAAC CAGAAACTTATGTCTCAATGTCAYATTCTATYAGATCATTTTATTCYGACATCCTCCAACATAAGATTT CTTAAAGCAATCCATCTAGTCATTTGCTTCCACAAACACAAGGTTCGAGATCATCACAAGATCCAAA CACAAACAGCAYACARGGAATGAGTTATCTAYCAAATAAAATTTGTSAGAAACATTTTCGGCT CAACATCATGCAATTAAACCAGAAACTTATGTCTCAATGTCAYATTCTATYAGATCATTTTATTCYGA CATCC TCCAACATAAGATTTC TTAAAGCAATC CATCTAGTCATTTGCTTCCACAAACACAAGGTTCGA Gm08:831GATCATCACAAGATCCAAACACAAACAGCA[C/T] 8314208 139 322 0.757 0.829 4208ACARGGAATGAGTTATCACATTCCCAACTAATAG AGAGAAACGAGACAATATGTAGATATACATATTATATAAATGAAATATARCTYACTYAAACATAGCT CACATCATTCCATCACTTATCGTGTAACATCACATCTCAACACTACACATCTCACACATTTTCACATTA TTTACGTRCTCAAGGATCGAAACACAATATYAGATCATTTTATTCYGACATCCTCCAACATAAG ATTTCTTAAAGCAATCCATCTAGTCATTTGCTTCCACAAACACAAGGTTCGAGATCATCACAAGATCC AAACACAAACAGCAYACARGGAATGAGTTATCACATTCCCAACTAATAGAGAGAAACGAGACAATA Gm08:831TGTAGATATACATATTATATAAATGAAATATA+A/ 8314292 [A/G] 140 323 1 0.715 4292G+ CTYACTYAAACATAGCTCACATCATTCCATCAC TTATCGTGTAACATCACATCTCAACACTACACATCTCACACATTTTCACATTATTTACGTRCTCAAGGA TCGAAACACAATATCACTCAACCAATCAATATCGAYCAATRCACAAGCGTTATGCAACAAATATACTA AGACTTAATCCTATATGTAATGTGGTATCAATCATTTTATTCYGACATCCTCCAACATAAGATTT CTTAAAGCAATCCATCTAGTCATTTGCTTCCACAAACACAAGGTTCGAGATCATCACAAGATCCAAA CACAAACAGCAYACARGGAATGAGTTATCACATTCCCAACTAATAGAGAGAAACGAGACAATATGT Gm08:831AGATATACATATTATATAAATGAAATATARCT+C/ 8314295 [C/T] 141 324 1 0.715 4295T+ACTYAAACATAGCTCACATCATTCCATCACTTA TCGTGTAACATCACATCTCAACACTACACATCTCACACATTTTCACATTATTTACGTRCTCAAGGATC GAAACACAATATCAC TCAAC CAATCAATATC GAYCAATRCACAAGCGTTATGCAACAAATATACTAAG AC TTAATCC TATATGTAATGTGGTATCATGTATCATTCCATCACTTATCGTGTAACATCACATCTC AACACTACACATCTCACACATTTTCACATTATTTACGTRCTCAAGGATCGAAACACAATATCACTCAAC CAATCAATATCGAYCAATRCACAAGCGTTATGCAACAAATATACTAAGACTTAATCCTATATGTAATG Gm08:831TGGTATCATGTYAGTGAAAAATCTCATC [A/G] GG 8314513 [A/G] 142 325 1 0.895 4513CGCCTAGAAGTATATGACAAGATAAACCACACA CTGGTAAGTCAGGTCACTCTCAYTAGATAAAATCATAAGGAGATTAGTTAGGGTCACTCTRTTTTGCG AGAACACTTCAATCATACGAAATCAACATAGGTTTCAAGGAACATTCAAACC GAGTATATTTAC CC CT AAGGCCTACACTCTAAAGAGTCCGTTAGGGATAAACCACACACTGGTAAGTCAGGTCACTCTC AYTAGATAAAATCATAAGGAGATTAGTTAGGGTCACTC TRTTTTGC GAGAACAC TTCAATCATAC GAAATCAACATAGGTTTCAAGGAACATTCAAACCGAGTATATTTAC CC CTAAGGCC TACAC TCTAAAGAG Gm08:831 8314736 143 326 0.8710.614 TCCGTTAGGACCTCTCCCTCTTGATTCAGGT[C/T] 4736CAACCTAGAAAATATTTTAGCACCYAGACTCTAT TTATGAACTGTACAAAACACYCGACTCCTCAATTGTTC TCAAAATAATTTTATCTCATCGC GC CTCAA AGTGATTAAACTCGTCGAGTTYCCACAATGGTTCTCATCACAATAC TC GTCGCACATTAAC TCATC GT TCTGAAAGGGTCTTATAGTCGTGTGGTGGTATTAGTTAGGGTCACTCTRTTTTGCGAGAACACT TCAATCATACGAAATCAACATAGGTTTCAAGGAACATTCAAACC GAGTATATTTAC C CCTAAGGCC TACACTC TAAAGAGTC C GTTAGGACC TCTC CCTC TTGATTCAGGTYCAACCTAGAAAATATTTTAGCACC Gm08:831YAGACTCTATTTATGAACTGTACAAAACAC [C/T] C 8314791 144 327 0.884 0.688 4791GACTCCTCAATTGTTCTCAAAATAATTTTATCTCATCGC GC CTCAAAGTGATTAAAC TCGTC GAGTTYCCACAATGGTTCTCATCACAATACTCGTCGCACAT TAACTCATCGTTCTGAAAGGGTCTTATAGTCGTGTGGTGGTAYGGTACATAACTCAAAACTCCATGCA CACAATATTTCAATACACATGTATTTTAATTCAAAC C GAGTATATTTAC CC CTAAGGCC TACAC TC TAAAGAGTC CGTTAGGAC CTC TCC CTC TTGATTCAGGTYCAACCTAGAAAATATTTTAGCACCY AGACTCTATTTATGAACTGTACAAAACACYCGACTCCTCAATTGTTCTCAAAATAATTTTATCTCATCG Gm08:831CGCCTCAAAGTGATTAAACTCGTCGAGTT[C/T] CC 8314860 145 328 0.912 0.715 4860ACAATGGTTCTCATCACAATACTCGTCGCACATT AACTCATCGTTCTGAAAGGGTCTTATAGTCGTGTGGTGGTAYGGTACATAACTCAAAACTCCATGCAC ACAATATTTCAATACACATGTATTTTAYAATTCAACAYGCAC TCAATTTATCACATAC GC TCAATC TC GTTATAATCTCAATATAACAATTTATCAGTTTATTCTAACCTCAATTGCGATAAACTCATCTC TTACCTCTAAGYAGGCTCACATGTGTAGTCYGACAACGATAGTGACGTTTCTAGCGATTTCCTAAGAT TCTTCAAAATTTTCCTAAGATTTTCTAACRTYAGAGAAAAAGAGAAAGGATTATAACCTATATTTCACT Gm08:831GTCTCCGTCTCCRTGCGAGGGACATTTC [A/T] CTA 8315543 [A/T] 146 329 0.825 0.7565543 AC TGAAGACATTGTTTCACAAATCC TAAYAGTGGGATTGTGAGAAAATGAGTTTYAAACCTGATTTTT AAATTTCACAATGATTCAATGGTTAATGARTCCGAGATCATAGTTTTAATGGRACAAGTTTGGATGTA TGCAGGAAGAGCATCTTGTGAGGGACATTGTTCTCACCACAGACATTATTTAAAAATTCCA ATTCTTCAAAATTTTCCTAAGATTTTCTAACRTYAGAGAAAAAGAGAAAGGATTATAACCTATATTTC AC TGTC TCC GTCTC CRTGCGAGGGACATTTCWCTAACTGAAGACATTGTTTCACAAATCCTAAYAGTG GGATTGTGAGAAAATGAGTTTYAAACCTGATTTTGm08:831 TAAATTTCACAATGATTCAATGGTTAATGA[A/G]T 8315644 [G/A] 147 3300.929 0.786 5644 CC GAGATCATAGTTTTAATGGRACAAGTTTGGATGTATGCAGGAAGAGCATCTTGTGAGGGACATTGT TCTCACCACAGACATTATTTAAAAATTCCAAC GATGGGAATGTGAGAAAATGAGTTTGGAACTTGGTG TTCAAATTTCATGATAATTCAATGATTAACGAGTATAGGATCGTAGTTTTACCTGATAGGTTT TAGAAATATATTATGTGTAAAATCTGATCTAATATRTCTATTTATAGATATS GTACTCTYAATTTATTA TTTACTCTAKCTTTTCTTTATTTTATTATTTTATWAAAAAAATTCTATTTTTACTCCCTATCAAATGAA TAAATAAAATATTCTTTTTTATTTTCCTTCAAAYTGm08:831 8316113 148 331 1 0.85 ATTATTTTAATTAATAAAATTATTTTT[C/T]CTAAT6113 TTATTTAATTATAAAAATCTTATTATTTTTCAAAAAC TC TATTTATTTTTAAATAAAATGCTTTTWAATT TATTTAAAAAAAGACGAGATGTTACAAATGTTTGAAGCACACTTTGCAATGTTATAAATGTTGACCTC AGACATCAATTGCAATATACACACCATAAAACAACATATGAAGTACACGTATGAGAT GC TC GAATATAATGAATC TAAACATATATGAAAAATCAGTAACTGACCTTTTCGACACAGTCACATGA ACAAACTCGCAGCAACAACGCATACACTAGTAACAGCAGTCARCGCACTCTCTTGAGAAAATTTGAT GTAAATGTATTTATAACTTTGTGACAAATATTTTTGm08:831 TTTC CC TCATTC CACACAGGAATAAAAAGT [A/G] T 8316689 [G/A] 149 3320.896 0.63 6689 CCAAGTGAGTGAAAGAGATGAGGAATAGATAGACWTCTTTCTCCTTATTTTAAAATCCCAAGAAACT AATTACCTAGAACATTTGTAACAAAAACTAGTGTTAATTTATTTC CATTTATC CC TTTTC TC TCTGC TTTATTTRTGGGAWGCTATAAAGAACGCTCTTCTCTC CTGAAAATTGCTMATTTAAGAAATTATTGTGAAAGAGATGAGGAATAGATAGACWTCTTTC TCC TTATTTTAAAATCC CAAGAAACTAATTAC CTAGAACATTTGTAACAAAAACTAGTGTTAATTTATTTCCATTTATC CC TTTTC TCTC TGCTTTATTTRTGGGAWGCTATAAAGAACGCTCTTCTCTCCTGAAAAT Gm08:831TGCTMATTTAAGAAATTATTTTCGAAGGA[A/C]C 8316899 [C/A] 150 333 0.895 0.7376899 ACATTTTAATCTGTTAGAAATAGCCMAAAAAAAATAGACAGAAAAATTACTCTAATTTTTTTTTTTTT TKGAATGATTGACTAGTCAAATTAACTCCAGTAAACAAACAAGCAGCGGCGGGTTGAACATGAATAA CTTTCAATATGCC CC TTTGTTAAGCTAAAAGATTAC CC TAACATGGAAGTTTATGC TACATATA CATTTTGTCATTATACTTTGCACGAAGTGGGTCATTGTAAGTCCACCTGTATTACAATTCAACAATAAC AAGAATGTCGAATAATTTTAGTATTTTACAGCAGTTAATATGTAAGTATAAAATGCTACTTGCAGTAG AAGAAAC CC TTTTTTCAGGGGAAGGGGAGGTC TGGm08:831 GAC TC TGGAGGTTAGTTGCAC GTTAAGCA[A/G] A 8317852 [A/G] 151 3340.924 0.776 7852 ATGAATC SC TATCATCAATGTGTTAACAAATCCAAAATTCTTGGTAAGGGAGAAATATCGGACAGAA AAAAAATTAAGATGTCAGAAAGCCAATGCAGAATTTTCTCAGCAAATACATTGAATGCTGCCTTAAC ATACTAAAAC CC CATTATTC GAAAGATGATTATCAATATTTAATARCATGACTGCAAGCCTATCA ATTATACTTTGCACGAAGTGGGTCATTGTAAGTCCACCTGTATTACAATTCAACAATAACAAGAATGT CGAATAATTTTAGTATTTTACAGCAGTTAATATGTAAGTATAAAATGCTACTTGCAGTAGAAGAAACC CTTTTTTCAGGGGAAGGGGAGGTCTGGACTCTGGGm08:831 [C/G] 152 335 0.924 0.923 AGGTTAGTTGCACGTTAAGCARAATGAATC [C/G]8317861 7861 CTATCATCAATGTGTTAACAAATCCAAAATTCTTGGTAAGGGAGAAATATCGGACAGAAAAAAAATT AAGATGTCAGAAAGCCAATGCAGAATTTTCTCAGCAAATACATTGAATGCTGCCTTAACATACTAAAA CCCCATTATTCGAAAGATGATTATCAATATTTAATARCATGACTGCAAGCCTATCAACCAACAAT GTTAGTTGCAC GTTAAGCARAATGAATC SC TATCATCAATGTGTTAACAAATCCAAAATTCTTGGTAA GGGAGAAATATCGGACAGAAAAAAAATTAAGATGTCAGAAAGCCAATGCAGAATTTTCTCAGCAAATACATTGAATGC TGCC TTAACATACTAAAAC CC CA Gm08:831 8318033 [A/G] 153 3360.912 0.809 TTATTC GAAAGATGATTATCAATATTTAATA [A/G] 8033CATGACTGCAAGCCTATCAACCAACAATACATGA AAAAATTCTGGTGTGATAAAAAAAATTGTGTAGACTCCTTTTAATGTCATAAAATCAGAAGTGTGGCA GAATCAGTCTAACATGTTACATCAACATTGAAAACATAAACAGATTCAGGACTCTGTAGATAATAAAT GTAGCATTTCAGATATTCTCAGAACAGAGAAACCCAAAAGTACTATGAAAACAGATGAGCATA AC TCATGAGCATGCACTTTTGTCAAGATCTCAAACCATATCAAGGGCTGCTAATAAACAACTCATTTA AATTGTGAGTTGTGACATGCAATATGATCCCTTCTTACTGTCCAGCTAAATTCACATAGAAGTCAAGG Gm08:831GAGTCAGGGTAAAGTTGACAAACTAAGAACG+C/ 8319087 [C/T] 154 337 1 0.857 9087T+TGTAAACAATAAACTTCAAGCCAAGTACATAT TTCTACAAAATGAATGCCAAAAAAATAAAATAAGATTTGTGAGATGGCATAATTATGCTTACTCTAA ATGAAATATGTCTTTTAACTATATTCCTTCCAATCAACTCTCCCTCTTGAACCTCAATCTCACCCACAA TCAAATTCCTAAATAAGCAAAATGATAGGTACTTCTCCCAGCCCAAGCCTAATTCCACCCTACCTTGTACACAC CC TTCTC GGGCTAATGTTCTC TGTC TTCTTACAACAAGCCCACATGCACTCCTCCCATGCTC TGCTACAGGGTTGACAGTTGGTTATATCTCTCTCCTAAAATTGATCAAGTGAACCTTTTGCCTATCCTT Gm08:831ACATACACCTTATTTTGTGATCTTGGG[C/T]CTTG 8319642 [C/T] 155 338 0.853 0.5319642 RGGCCTCCATCASAAAACCATTCTTCATAAAAACTCTCATTTCACTCTTCTGATGACTAATAGCAGAA AATTTTTTAGATAACAAGAGAAAAAGAAATCTTAAATGAACATTTCACTATTGRCATGAGCATCTCAA TATCATCACATGAATC CGAGATCATTTTGGAC CAGTGCCATAGCAGATGAACTTCATAAG CCAGCCCAAGCCTAATTCCACCCTACCTTGTACACACCCTTCTCGGGCTAATGTTCTCTGTCTTCTTAC AACAAGCCCACATGCACTCCTCCCATGCTCTGCTACAGGGTTGACAGTTGGTTATATCTCTCTCCTAA AATTGATCAAGTGAACCTTTTGCCTATCCTTACATGm08:831 ACACCTTATTTTGTGATCTTGGGYCTTG[A/G]GGC 8319647 [G/A] 156 3390.853 0.587 9647 CTCCATCASAAAACCATTCTTCATAAAAACTCTCATTTCACTCTTCTGATGACTAATAGCAGAAAATT TTTTAGATAACAAGAGAAAAAGAAATCTTAAATGAACATTTCACTATTGRCATGAGCATCTCAATAT CATCACATGAATCCGAGATCATTTTGGACCAGTGCCATAGCAGATGAACTTCATAAGTAAAT TTTTTCTCAGGATAAAACAACAAAAAACTAATACCAAAGAATAGAATAAACAATCTACCACTATTCTT GAAACCGAAAGATATAGAACATAGGAGAAATTGAACTTACGGGTTATTCCAATCAGTAGTATCCTCA TTGACAAGATGGGTCCACTTGGTTCTTCCACTACGm08:832 GACCAAAGTGCTTAACTTGCATAACCTTTGG[C/T] 8320068 [C/T] 157 340 10.837 0068 AATATTGTCTTGTCCATTTTATCCTCCCCAGTTGGGGCAGAGAAATCACGAGCGAAAATACCATCAGA TCCAACGGTGGCAGCTCGGTCATCAGATTCATTCTGGAAGAAAGCACCTTTGTGATAGTATTTCTGCA TAAATCTCCATTTCTGCTTTGGTGGTGGAGCAGGTTTGGGATTCCTCCTTTCCCACTCCCTCCT TCATCAGCCCATTCAGGAACTTTACCGGGCCAATAACGCTTAACTTTAGTTTGGCCAATTTTACCTCTG AGCTTATCCCTAATGGCTATTACAGTATCACTAACACCCGCTGTCACCGACATTGTTCTTCCTCAATTG AACGCCAAACCCTATATTGCACAGATGCATAGTAGm08:832 8321253 [C/A] 158 341 0.919 0.773AATCGGTAAAATGTTTGTTTACACAGCA[A/C]AG 1253AAACAGAAGATTCCAGATTAAATAGCAAGAAAA TAAATAAATGAATCAAGAAACACAGAAAGATCAATAGTGAATGATAAATTTTGATATGCGAAACATT GGAAGGGTTTGTGTTCSAAACACTAACACTTGAATTGTTAGAGAGAATAGAAGAAAAGTTWGAAGGA CTTACAATTACAGCGACCGGAAGGAACCCTCCCCTCTCTGTCTCTGTCCCGTTCCAGGCAGCGCGT CGCCCCACCCCAGCTTGTTCTGTGAACTTTTATTTGATTTACTTTCTATAGTATTTATTTTTGTTTTTATG AGTATGTAAATGACATCTTTATACGAATATTATGTTTTCATTAAATAATAATAATAATAAATTTCTTAA Gm08:832AATTAAATATATATACACTAATGCT[A/C]ATAAA 8321649 [C/A] 159 342 1 1 1649AAAATTGAACGAATATCATATTTATTAAAACTAA TTTTTTTATACTAAACTAAAAATAATTTAAAATTTATTATTATTATTATTATAAAGATATTTAAATTTTA TATTTTGGAATTGTATATATAAGATAAAATACATTTAAGTTTCCTAAGTTACAACTTTCGCATCGGTTA CATTTTAMAGGWTATATATATAATGTCTTTGTCCAAGGCTTGCTAACAAAAAAGGA GATTGCAAGATCAATAAAATACCTTACAATAATGAGAGACAAAGGGTTTTCAGTAGATGCTGCTACCA CAGAAATTACTATCAACTACTTATCTACTAATGAAGGAGACACCAGAATTCGAGAATTTTTTTTTCCA Gm08:832AAA AGATAGCAAATGCCAAGAGTTTCACTT[A/G] 8323937 [G/A] 160 343 1 0.918 3937GACATTTATTCAAATCCTGACTCTCAATTCATCCA TGTTCCACAATCCTATAGGACCCCATAGAGAGAACTGGCATAGGCTTCAGAACTTACMATTTGTTAAA TATATAAAATCATTACCATTCAAGTGCWTCCACCTGACAATTTATGTGATTAGGAGAGTTGGTCCTTA ACAGGTATCACAACCTTTAAGAAATTATGTTGATCCTTGTTGCTTCTCTTCTTCATAATTAACT TATATTTGAGCCCAAGGTAAAGTGGGTTTGTGCATTGTCCRCACTTCAAGCTCAAAAAGCTCTGTTTTA AGGGGGTCTTAGATATAAATCTTTCTTAGCTCCACCAATCAGCTTAAGCTGTGAATAGAATTGTTC CT Gm08:832TGACATTTTTAGTGGTAAGTATTTTCAC +A/C + TC T 8324341 [C/A] 161 344 0.9290.787 4341 GC TTGCACATTTATTTTGATATAACC TCAAGTTATTAAAATAGCTTAAAAAAATAGACCTATATACAAT TTAGAAATTGTGCTGTATCCTTGCATTTTTATGGAAC TGAGTAATTTTTTAC TTATGTATATTTGC CTTCAAGTAAGTTTAATAATGAAGCAAGTTGCATTAGG GATAAGCCAATCAATATTGCTAGTTGTTATTTTATATTTTGTTTCCTTTCTTGTGTATTT TACTTTTCTGTTTTAGGAGGATTCCTGATCCTTCTGCACTGTACTCCTTTTCTCTCCTAGTTCATTGTTT GTGATGGGAAWTTTTTTTCCATATTTATTACCTGTTAGGAGACGAAAATCTAAGATCTAATTTATGGAT Gm08:832GC TTGC TGTC CTTTC TGCAAAC GTN[A/T] TTTTTTT 8325127 162 345 0.829 0.7065127 TTTTTAC TTTTGACAGTTTTCC CC CCATTTAAAATAACAGTTTGACTTCATGGTTCTTGGTTTGCAGATT GAAATCACTYTATGCACTCATTTTGTTATAACTTATGTGCGAGGAAGACCGCAAATAGTTCAGCGATG GATCATAGAAGGTTAGTCAAACATTTTTTCTTTGCAATATCTGCTCAGCTTGTTT CTCTCCTAGTTCATTGTTTGTGATGGGAAWTTTTTTTCCATATTTATTACCTGTTAGGAGACGAAAATC TAAGATCTAATTTATGGATGCTTGCTGTCCTTTCTGCAAACGTNWTTTTTTTTTTTTACTTTTGACAGTTTTCC CC CCATTTAAAATAACAGTTTGAC TTCATG Gm08:832 8325214 163 346 0.9290.837 GTTCTTGGTTTGCAGATTGAAATCACT[C/T]TATG 5214CACTCATTTTGTTATAACTTATGTGCGAGGAAGA CC GCAAATAGTTCAGC GATGGATCATAGAAGGTTAGTCAAACATTTTTTCTTTGCAATATCTGCTCAGC TTGTTTTTTGTAATTCAAATTTTTTAGCATCATAAGTTGTTCGTTTGAAATTTTGAATGAATATTTATCT GTTAAGTTATATTTCACTTTTCTAATATATTTATCTCAGAATAATGCTTTGACTTTTACAATGTTCC CC TCACAAAATTGATC TCTTTAAAA AATAAAAAATAAAAACTTTGGAGTTTGTCCAGCTTGGCTCCAATCTTAACCAAAGCAGCATTAAAGCT TTGAAGTATAGAGCAAAAGTACACCATATTAGGCGm08:832 TAATCAATGAAAAGGTACAAAGCTC CC GT [C/T]A 832606 [C/T] 164 347 10.768 6696 GATTTTGAACTAGRCAGATAACTAAGNGAGTGTTTAGTTTGGTTGTTTTTTGATTTTATTTTCACTGAA AATARAAAACGGTGATGAAAATGTGTTTGGTTTGATTTCTGAAAACATTTTCRGTAAAAATGAAAACA GTAAACAACTAGAAAATGAAAACAAAAAATTTTCGTTTTCAGWATTTTCAGTTGAGAACAGA AAAGGTACAAAGC TC CC GTYAGATTTTGAAC TAGRCAGATAACTAAGNGAGTGTTTAGTTTGGTTGTT TTTTGATTTTATTTTCACTGAAAATARAAAACGGTGATGAAAATGTGTTTGGTTTGATTTCTGAAAACA TTTTCRGTAAAAATGAAAACAGTAAACAACTAGAGm08:832 AAATGAAAACAAAAAATTTTC GTTTTCAG[A/T] AT 8326877 165 348 0.8840.808 6877 TTTCAGTTGAGAACAGAAACCTCATTTTGGTTAAAATGAAATTGYGGTGACAATAAATGTAGTTTTAA RCAAATCTAAAAATACAAAAAGACAATAAGTCAATATATCATAAATTTTCAGTATTTTTATTTCATRA AAACAGAAAACAAGAAATCAAACCAAACATRTTTTCAGAATTTAAATCTTTTGAAAATAAAA TCTCTTCAAAAGCCAAGTCCTTGGTTAGGACAGTGGTACTTAACATGGTTAATGCAAATGGTTTGTWG CAAATTCATAATAGACCTTTCAACCAGCTTTTGGCTCATTTTATTGCATTAGTCTTATTTGTTTTGGAG AATTTCTTTTATTTTTTTGGTAACTAGCAGATTTCGm08:832 TTATC CTC CTC CTAGTTGTGC TTCTC TT [A/T] TC TC 8328633 166 3490.919 0.651 TTTAATGAATTTCCTCCTATGTAAAAAGCAATAG 8633AAAAAGAAAACCAGTTTTAAAAAAATAAAATAA AAGAACTAATTTCAGGTACCTTCTTCCATTTTGCAATTAGATTGCGGTCAGCATATCCTTGATCTAAAC AGAATTCATACAGTTCTTTAGAAATTTCCTTCCTCCGATGGTATAGATCAAATATGTAGC TAAGTAAATCTAGAAAATATATAACTTTTGACAAAAAAATTATATCACTATTTAAATATATCTTTTTTC CTTTGTTTCTTATTTCCTAAATAAATTTTTTTATTAAATTTATTAACAAAAATTTCTCATAATTAACGAA TGAGGTTAAAAATAATAAAAAAATGAYAAATATAATAAAAACAAATTAAATTTAAAGAC TT [A/G] AA Gm08:833 8330929 [G/A] 167 350 10.789 ACATAATTTTTKTGTCWCATGAAAATATTTTTTTT 0929ATTCTAAACAAATTGTTTAAAGATAATRAAAATA TCATTTTTTTAAATCCTAWAAATATACCARATAACTATAATTATTTAAATTAAATCACTCTAGCATAT ATTTTTAATAAATCAAATTAATATATACAAATATTTTAATTTACTTTAAATTTAAAGATAA ACATAATTTTTKTGTCWCATGAAAATATTTTTTTTATTCTAAACAAATTGTTTAAAGATAATRAAAATA TCATTTTTTTAAATCCTAWAAATATACCARATAACTATAATTATTTAAATTAAATCACTCTAGCATAT ATTTTTAATAAATCAAATTAATATATACAAATATGm08:833 8331132 [C/T] 168 351 1 0.657TTTAATTTACTTTAAATTTAAAGATAATA[C/T] GA 1132TAATATAAATATAGTAAAATTTTATAGAATTTTT AAACAATATTTTYCATTTATCTTTTTTTTTTCTTTTATCTCTCTAGTTGCATGGAGCATGAGCCAACTTC CTAGTTTATTGTATATTTTCGTGATAATGTTGTGGCATTTGTTAGACATTTTAAAATATTAAATCTTATT AATTATTTTWAAATCATATTTATAGTTTAAAGATAATRAAAATATCATTTTTTTAAAT CC TAWAAATATACCARATAAC TATAATTATTTAAATTAAATCACTCTAGCATATATTTTTAATAAATC AAATTAATATATACAAATATTTTAATTTACTTTAAATTTAAAGATAATAYGATAATATAAATATAGTAA Gm08:833AATTTTATAGAATTTTTAAACAATATTTT[C/T] CA 8331181 [C/T] 10 352 0.87 0.6121181 TTTATCTTTTTTTTTTCTTTTATCTCTCTAGTTGCATGGAGCATGAGCCAACTTCCTAGTTTATTGTATA TTTTCGTGATAATGTTGTGGCATTTGTTAGACATTTTAAAATATTAAATCTTATTAATTATTTTWAAAT CATATTTATATGAAAAATATGATTTTTTATTTAATCTTTCTAGAAAAATCTTAATGTAT TCTCTAGTTGCATGGAGCATGAGCCAACTTCCTAGTTTATTGTATATTTTCGTGATAATGTTGTGGCAT TTGTTAGACATTTTAAAATATTAAATCTTATTAATTATTTTWAAATCATATTTATATGAAAAATATGAT TTTTTATTTAATCTTTCTAGAAAAATCTTAATGTAGm08:833 TCCACTTCCAACTTTTACATTTAAAAT[C/T]CCATT 8331408 [C/T] 170 3530.842 0.771 1408 ATATATTTTTTTTCTAATTAACCTTCTCTAACAATTGTTCAACACTTTCTTCCTAAACCTCTATTTCAGTTTC TCTC CC TCTTC GGTC TTCC CATTGAATTC CAGGATTTTACATACAAAAAATTTGWTAGTTTTGTTG TCTTGACAAGTTTTCGGAGGATTTGTTAAATTC TAAAGGACTTATGCACTACGTTG CGTGATGTCACTCATCTCATATTATCTATTTTGTGAC TAAC TCATGAATTTATGATAGATTGATGATCG GTGATTTTGGCCTACTACAATAACAATTTTAACTTTTAAGGAATAATC CC GAC CACTTTAAGGTATATTAATATATTAATTATTTTTTTCTCCAATCTTAATTT Gm08:833AATTTGTTTGATGGTAATGAATCAGAT +A/C +AAC G 8331827 [C/A] 171 354 0.8380.772 1827 ATTTTGGGACTGTTGTTGTTGTTCCATTTTCAGTTTTTTATTTTGTTTATGACTAGTTGAGTTTGYAATC GGTTCTTGCTCGGTGATTTTAGAGGTTTTGGACATGATTTTAGAGTATGTTGTATTGTGTAAAACTTTGT TGCAATCTCGTGTGGTTAAATGGGTGTTAGGATGTGAAAATTTTATGTCTAAAATT AATACACTTGTGCATTCAAATATCCATAATAGTTAATAACAACAACTTATTCAATATACTATATTATC TAGGGTCACTAGATTAAACCCACTTCTAAAAAAATCTTAAAACATCCAAATTTTATTAATACGTTATCT TGAACATACTTTCTTCTATAAATGTTAAAATTTATGm08:833 TTGAAAATTTGAAATCTTAGAAGGTCTC [A/G] TAC 8332651 [A/G] 172 355 10.836 2651 TTTAATTAATAAATATCTTTTATAATTTTTMATGAATAGTACAATCAAGTGTGTTAAAAAATATTTTCT TGAAACTCCTCTAAATTTAATGCTACAAAAATTACTTTTTCTTGCTTTCTCTTCAAACTTAGTGAGCAT TTTTGCACTCTTAAATTATGTTTGTCAAAATATTTGAATTGATTTTTAGTTTTTTTATT AATAACAACAACTTATTCAATATACTATATTATCTAGGGTCACTAGATTAAACCCACTTCTAAAAAAA TCTTAAAACATCCAAATTTTATTAATACGTTATCTTGAACATACTTTCTTCTATAAATGTTAAAATTTATTTGAAAATTTGAAATC TTAGAAGGTCTC RTAC TT Gm08:833 8332685 [C/A] 173 3560.857 0.772 TAATTAATAAATATC TTTTATAATTTTT [A/C] ATG 2685AATAGTACAATCAAGTGTGTTAAAAAATATTTTC TTGAAACTCCTCTAAATTTAATGCTACAAAAATTACTTTTTCTTGCTTTCTCTTCAAACTTAGTGAGCA TTTTTGCACTCTTAAATTATGTTTGTCAAAATATTTGAATTGATTTTTAGTTTTTTTATTAACAGAAAAG TTTATTTAGTTGTTTGATAAAGAAACTTTTTCTTGCTTTCTCTTCAAACTTAGTGAGCA TTTTTGCACTCTTAAATTATGTTTGTCAAAATATTTGAATTGATTTTTAGTTTTTTTATTAACAGAAAAG TTTATTTAGTTGTTTGATAAAGAAGTTTTTTAAATAATTTTTAACATTTTTTTAAACACTACTTCAAGTA Gm08:833ATATTTTTWAAAATATTATTTATTT[C/T] TTCATAT 8332957 174 357 0.902 0.787 2957ATTCTYTTTTTATTTATTTTTAATATATTTATCAA ATTTATTATTTATCCTTTTTAAGCAAATCATTATTTTATTATTTTWAAGTTATTTTATATTTTTTAAC TA TTTCAAAAACTAATTTTATCACACACTTAATTTTAATAAATTAATTTTTTAACTTCCAACTAATTTATTA GTTTTCAGCTAATTTTATTGATTTTTCTGCATCTGAAACAATTTGAAATTTCA AAATTTCTCTTTTCTTTACGAGGTCATCAAAGCACAAAGC TAACAAATTC CC TAGAAGAGGGTGCATA AAACTCCAACCTGTTTCCTCTGTTTTTTCCCTTGCAATTATTACTCTTTTTTATTGRTAGAAATTGAATT Gm08:834RTTGAARTATAAATGTGAAATAAAGTC [C/T] CAC 8343167 [C/T] 175 358 0.904 0.8833167 ATCCAATAAAAATAAAAAAATTTAACATCATATAAGTAAAAATAACTAAATCTTAAAGTTTTTAAATT GC TATTCTC TTTCATGTAAAGATAAAACACATAAATCTAACTCTTAAAGTCTCTTGATTACTATTTTTC ATCTTTCATGATATAAGTGATGATTTAGCCTCTAGATTTCATGGTGATTATAGAAGTGTA CAAGATAGGACCTTTTTACTTTGTTGGTCTATTAATATCCAAGTTGTTCATGCTTATTTTCACACCTAAC ATTAGCTTATTCAAGATTCTTAATAAAATATTAGGGAAAATATCATGAAACTTTTATCAAAATTGTTT ATTTGTCGTTGACGTTTTTGGAAACATCTCAATAGm08:834 GTGACTTGTTACTCAATCAATCTTTACT[A/G]GCA 8345187 [A/G] 176 3590.933 0.799 5187 CTCTCATACTTGGTTTTCGTTATTCCTGTTTTCAAACCACATACTTTGACTAATGGACTATGAATGAGG CTGCGTATAAAAATACAATTGGCGTATTCGAGATGCAAATTGTGTTATTGGCCTCTTGTCCTTTTCCAG ATCAGTATTGAGAAGTTCAGGCAAGGCTTGTATTGAATCTGACTCTGACAGATACATAA ATACGACTTTTWCTTGTTGCCACTCTTTACCAACAGCATTCAAGACGTACGTTAGGATATTCAAATCC AATGCGTCACTGAGGAACTTTTGCACTCATTTTTTCACGCAAAAACAGAGAATCATCCAGCACAGAGT CTTGCAAAAATTGATGTGAAACAAGAATGCTCTGGm08:834 AGCCTAAATTGGATCAATGTGCATGCTAAA[A/G] 8345720[A/G]177 360 0.8710.587 5720 TTTAGACCCATATMKTATKGGGAAGTTTTTATCCCTTAGTCGCTTTTGTCTTTTTCCTTTCCTTTTTCTA AGCAACAAACCATATTGTTTTATAATTTGGGCGAGGTCTAAATTCGTTTTATCATTGTAACAAAAACT AAAGAAATTAAAGCAAACGATTTCATAGGCTATTTGGGAGCTATGTTTTATGAGGTTAATAA AAATTCGTTTTATCATTGTAACAAAAACTAAAGAAATTAAAGCAAACGATTTCATAGGCTATTTGGGA GCTATGTTTTATGAGGTTAATAACAAAATAGGAATCTCTTGATTTTAAGAATGAACAATTTTTTTTTCA CTATGAAAGGAGTCCTGAACATTATAATTGGATTGm08:834 8346030 [C/G] 178 361 0.87 0.721GGGTGTTAAGGAGAGAAATAGAAAGGAGA[C/G] 6030ATTTCACTCGATTGGTTCARAAAGAAATAAGAAC GAAATTGACAAATTCTGTGGGTTCATTTGGGAAATTCTTCTCCATTGTTCATGATTGGAAATGATTTTG TGTATCTTCTTTTTTTTTCTTAATTTCTTTTTAAAAAATCAAATAATTTTTTTWAAAATAATTTCTTTATT AAAATACTTTTACTTTAYGATAAATAACAAAAACTAAAGAAATTAAAGCAAACGATTTC ATAGGCTATTTGGGAGCTATGTTTTATGAGGTTAATAACAAAATAGGAATCTCTTGATTTTAAGAATG AACAATTTTTTTTTCACTATGAAAGGAGTCCTGAACATTATAATTGGATTGGGTGTTAAGGAGAGAAA Gm08:834TAGAAAGGAGASATTTCACTCGATTGGTTCA[A/G] 8346050 [A/G] 179 362 0.929 0.7186050 AAAGAAATAAGAACGAAATTGACAAATTCTGTGGGTTCATTTGGGAAATTCTTCTCCATTGTTCATGA TTGGAAATGATTTTGTGTATCTTCTTTTTTTTTCTTAATTTCTTTTTAAAAAATCAAATAATTTTTTTWA AAATAATTTCTTTATTAAAATACTTTTACTTTAYGATAAATACTATGAATTAAAAAGATAAA CTTAATTTCTTTTTAAAAAATCAAATAATTTTTTTWAAAATAATTTCTTTATTAAAATACTTTTACTTT AYGATAAATACTATGAATTAAAAAGATAAATATATTCTCTTATTTTCTTATTTCTCTTCCAAGGATTGT CGAGATGGGAGAAGATTAACGTAAAGAATTTTTGm08:834 ATTTTTTTATTAAAACAGCGAAAATATAG[G/T]GT 8346352 180 363 0.9360.841 6352 ATATATATAAAAGGCACAAATGGGTGCCCCCAATCAATTACAAAGTGGATAAAAGTCCAACAAAGAT AGTATACCTCGGTTACACCATATTAACAAAGGAGAGTAAATATAGTTTAACCAAGGCCAAAAACATC ACTCCTAGCCACACTCCAGTAAATATAGTTTAACGTGAAGAATTTGATTCAACTTGTGAGAGCT AAGAATTTGATTCAACTTGTGAGAGCTTCACCCCTTAAGTTAATTCACCATATAGCTCAAATCGGATT AGTTGGAGAACTTAATTACCCTGATTGCCCTTTCTTAAAAATATTGCAGAAGCACCAAATAATACCAC AATGTGTCGATGTGTTTCCGAAACTAGATGATAGGm08:834 ATGGGTAGGAATTTTTTTATTTTCTTTGAT[A/G]T 8346726 [G/A] 181 364 0.870.8 6726 ATTGAAAAGGCAGAAAGAAACACAAATTTTAGTATTTAATAAAGCAAAATGCACACATCCCCCAAAC AAAACAAGCCTTATTCAACCCAAATTGGTTTCATATCACAGAAACCAACAGGATGCCGCCTTCCTCCT TACTGGTCCCACCCACTCGAACAAAAGTTSTACAGAAATAAAAATGGCTACAATTCTTCTACCA AGAGCCTGAAGGGCACAGATGGGATCAATCTCGGTCACGATGACACGAGCACCAGCCTGCTTCATTG CAGCAGCACAACCCTTGCCAACATCACCATATCCAGCCACAACAGCCACCTTTCCAGCAATCATAACA TCGGTAGCCCTCATGAGACCATCAGGGAGAGAGGm08:834 TGACGGCACCCATACAAGTTGTCAAACTGTTA+A/ 8347799 [C/A] 182 365 0.9190.757 7799 C+AAAACCACAGATTAAAAGGTTAAACAAACAAAACACAAGCAACAAAGCAAAATCCAATTATAATC AACTAGATCCATGACCAGCTAGTATAATGTCCTCAAAATCCAATCACCCACTTCTTACTTTCAATACC CTAATCAATAAACAACCCGTCACAAAAGACTCGGTTTGGATCAATGTTTGCAAAACCAATTTTGAAT AACAAACAAAACACAAGCAACAAAGCAAAATCCAATTATAATCAACTAGATCCATGACCAGCTAGTA TAATGTCCTCAAAATCCAATCACCCACTTCTTACTTTCAATACCCTAATCAATAAACAACCCGTCACAA AAGACTCGGTTTGGATCAATGTTTGCAAAACCAAGm08:834 8348022183 366 0.854 0.848 TTTTGAATGAAAACGATTTCGAGTTAAAAT[A/T]G8022 ATTTYGAAACAACATGATTTATGTTTGAACATTTTTTTATTTTAAAACCAAAAACAGTAGTAAAATTC AGTATAATTTATTTTATCCTATCCAAAAGTAGCTTCAAATCAAAATGTGCACTCAGAATCAATTCCTTA TTTGTGTAATAAAACATGTGACCATTTACCTAAAGTCACGTTAGCAAGCAACTTACTAATGT CAAAACACAAGCAACAAAGCAAAATCCAATTATAATCAACTAGATCCATGACCAGCTAGTATAATGT CCTCAAAATCCAATCACCCACTTCTTACTTTCAATACCCTAATCAATAAACAACCCGTCACAAAAGACT CGGTTTGGATCAATGTTTGCAAAACCAATTTTGAGm08:834 ATGAAAACGATTTCGAGTTAAAATWGATTT[C/T] 8348028 184 367 0.844 0.7878028 GAAACAACATGATTTATGTTTGAACATTTTTTTATTTTAAAACCAAAAACAGTAGTAAAATTCAGTATA ATTTATTTTATCCTATCCAAAAGTAGCTTCAAATCAAAATGTGCACTCAGAATCAATTCCTTATTTGTG TAATAAAACATGTGACCATTTACCTAAAGTCACGTTAGCAAGCAACTTACTAATGTTCTGAC AMTATGAAAAATTATACTTCAAACAAGTCTCTCATAAGAATGTTTATGGTCTCATACAGATGAATATT TTCACTTCGAATACACGTAAAACTAATATGAATTCACACAAGTGATTAAAGATCTAAAACTAACTTTT GTCTTCTTTTTTTTATAGATGTGGGTTTCATTCTCTGm08:834 ATCATGCCACTAAAACTATCATCTAATA[G/T]ATT 8349925 [G/T] 185 3680.929 0.717 9925 CTTTGACATCTAAGGACTAATTGAATAAATACAATTAAGTAAAATTGTCTATGATTTAGGCCTGTGGA ATAATCCTTGAGTAAGCCTTTATTGACATCGCTAACAAGTAGCATGTCATTAAGGTTTCATTCGATGG TATTGATCAGGCCTCTATAAAATTTTGTACATTTTAATATGCATCAAATGAGCATACKGGT ATAKATTCTTTGACATCTAAGGACTAATTGAATAAATACAATTAAGTAAAATTGTCTATGATTTAGGC CTGTGGAATAATCCTTGAGTAAGCCTTTATTGACATCGCTAACAAGTAGCATGTCATTAAGGTTTCAT TCGATGGTATTGATCAGGCCTCTATAAAATTTTGGm08:835 TACATTTTAATATGCATCAAATGAGCATAC[G/T]G 8350122 186 369 0.9290.649 0122 GTAAAGATTTCGGTGCTCAAGTTAATAGTTGGTAAAGTAAAAGCATTATATGTAAGATTTTCATGTAC TTGKTAAAGCTAAGGGACTATCGGAGATTGTTGATAAGCATTTAAAAAACTCTCAACAATCTTCTATC TGCCTATAAAGTTTTCTYAAAAAGCATTTAAAAAATTTATAGGTTAATTAGAGATTTGTTAGG CTCTATAAAATTTTGTACATTTTAATATGCATCAAATGAGCATACKGGTAAAGATTTCGGTGCTCAAGT TAATAGTTGGTAAAGTAAAAGCATTATATGTAAGATTTTCATGTACTTGKTAAAGCTAAGGGACTATC GGAGATTGTTGATAAGCATTTAAAAAACTCTCAAGm08:835 CAATCTTCTATCTGCCTATAAAGTTTTCT[C/T]AA 8350277 [C/T] 187 3700.929 09 .0 0277 AAAGCATTTAAAAAATTTATAGGTTAATTAGAGATTTGTTAGGTAGGTTAACATACATGTAAAGATTT TTCTTTTTTTGGAAAATACATGTAAAGAGTTTTGTAAAAGTAGAACTTGTGAATACGTGATTTATAAGA CAATTCATATTCCTCCCAATCAGGTAATTTTGTGCAAAAAGTCTTATTAAGTTGGTGTGTA ATATTGTAAAACACAAAATATTTATATTCCAATCTTMAATGTTTTTATTTGACATTATAAATATTTAAA GGATAGAATCAATGTTAATCAAGTTAACATAAAAAATAAAAAATTACATAGCATTCAACATGTAGGTA TCAAATCTATGTTATAAAATGTTTATTAGATAGAGm08:835 8351061 [G/A] 188 371 1 0.823GAAAAATATTTGCTAAAATTTWGATAATT[A/G]T 1061GCTATGTTTATATGTTGAATGATGGGTAAAATAA AATGACGCATAATTAAGTAACATAAGTAAAATAAAAATTAAGTTTAATTTTTATGAATTATCAATAT AAAAAAATAAAATATATTCCTAACATTTCTCTTTCCTCTATTTTACATTCATTTTATTTTCTTAATTTTT TTCATTTTGATATCCTTTAATATAATAACCCGGTCAAAATATAGGTTTAACAATTAGTCAAT TACTATATAAATAGGTTTTGTATTTGAATATGTTAGTAAAAAGTAGTTTTAATATATCTTATTCCAGTA AAATTATCAATTACTTTTAATAATAAAGTCATACAAATTTGTATAAAACTATTTTCCCCCTACGATAA Gm08:835AAGTTGTTTCGAAAAAAAAGTAAGTTGGA[A/G]A 8351503 [A/G] 189 372 0.869 0.7181503 AATTTATTGAAGTGATGAAAACTATTTTTATGGTTATTTTTTATCACACAAATTAATTTTGGAATCTTA TAATTAGAAATGGTTGAATTTATATATTGGTTAACTTTATTTTCTTATTTCGTCCACAGTAATGAATTG TTTCAAACAAAAAAAAAATCAATTAATATATATTTTATAATTTTACTATTGAAAAATACCT AGCATAATCACAATTATTGAGAAGATATTTTTATTTTATTTTTACCGAATCGTCGCACGACTCGGCGT GTTGCAACCGCATTAAATCTTTGTGTTGGTCTCACCCTGTCTTTTTGTGGATGATCGATCCTCTTGGATT GGTTTTTATAAAACTCAACTTCCCATCGGTGTTCTGm08:835 TTAGTAATTGGAGTATCTTTGGATGTT[C/T]GTTA 8352313 [C/T] 190 373 10.743 2313 CATTTTATGATAAATTTAAATGATCCACAATCACTAACTCAATTTTGCAAAGCAGGATTCTGAATGTT TTTGTAAATCTCGTTTTGTCCTAAAAGTTCGTCTATAACAATAAAACAAACATGCACTTGGTTGTTTTT AAAATTGTCTCAAAACTCTGTTATAAAGAAATAAGACCTAAAGATATTTTTTACAAATT ATATCCTTAGATTAATTTATTTTSTTGATAAAAAAAAWKGATAAAAATTTCCATGCTTTAAATTTGTCATTGGTC CATC TGATC GACTC TATACATCAAAC TTGAGTGTTATTTGCATACAAAAGGAAAACATCAG AGACATGACAGAGTAGGTTGCATTGGTGTTTAGTGm08:835 TGACCTGATTAAGAAGTTACACACAAAGTG[C/T] 8352743 [C/T] 191 374 0.8430.72 2743 TCC TCTATC TC CTC TTCAAGGTC CTC CTACC TATAGTCTTCTTGTACCTCTTATTATATGGATTAATTAG TGTAGAATTATTTCAACTTAATTAATAATTTTGAATTTAAGTCATGAGAATGAGTATCAAAAYTTTTTC AC CTATAAAAATC GAATRTGCTTCAAATAAGATTGTCTCTAATAAATAATATGTGTTTAAT AAACCTATGTCGGTTGGTTCCTCTTTAAAGAAAAGAGAATAAAAATAACAAAGAAAAAAAAGTCGCC TTCCATTTCATTCGCATTCATAGTAAAAGAGTGAGC GATC CC GGGAAATGAATTAATATACGAC TAA AAAGATTTGAGAATTATAATAATTAATAATTAATGm08:835 AATTCTTTTTCAAAAGTAAAGTACAGTACTGC +A/ 8353341 [A/T] 192 3750.812 0.774 3341 T+GGAAACATGAGCATGTTCATAGATTAAAATTTAAAAGAATATTATCAGTAACAAAAAAATAAAAA TTAACCCATGCATCCAAGAAAGAAATACYCATGTGC TTCAGTTGTCC GC TGTC TGAGATGTGGTGACCTTTTTTCAAATGATCATAATAGTTACTTCATAATG AC GACATGCATCAAAC TATTTTTTC TTCAAAATATCCCCCATGTTAATGAAGCAAGGTGTGGGGGA AGGAAAGAGTCAGCATCAGTGAAGTAGAGAGGGGGGTTGGTGATTTTGGTGGGAATAAATTGGCTATATTGC CC CCACCAACC TC GTTGC TAC CAAATAC CAACAACACTGACTCACTGAGAATTGGGAAAGAA Gm08:835 8355175 [C/T] 193 376 0.8670.787 AC TTAAAAC CAAGTCTTGCAGTGAC GTACATG+C/ 5175T+AGTGTGTGCATCACACATTCAGGTTTCCAGTCAAATTGTAGAACAAATGAATTTC TTGC TTTAAC TT AAGTTGAAGTTTAAGAAGTGAAGCTGATGCTTGTTTTTGAATGAAAAGCCTTTGATAGTTTGATGTAA GCATTTTCCAAATTTAACTCTTCCCATGCTTGACAGAGCCAATTAAGCTAACTGGTTTGATAACA CACCCCTCATTAGAGGCTTAGGATTTTTTTGAGTCCTAGAACACACATCTTATCTCAATAATGATTTCT ATCATTGCCAGAATTACAATTAAAAACTAAAATATAATCAATTAGATTGAATTGAACTTCTACAGACC CCAAAGGCACTCGATGCATTTTCACTGTATGTGGGm08:836 TTTGTCTTTC TGTAC TATAC TGCAC GCTT [A/G] GC 8360133 0133 [A/G]194 377 1 0.773 AAAATAATCAGTAACACATGTTAAGAGAGCTTGCAC TTTATTTTTATC TTGTTGAC GGGTTTGTTGTCATTGAAAACACATTATATTCAGAGGAATTTGACTC AACATGTTCAACCCACCAATTATCACATTTAAACAAATYTAAATCAATCGCAAATCATATATATTCAG AATTTTACATATTAAATATTTCATATCAATAACATGGTTATGTTGAAAACAAAAGAAAAA AATATCAAATTTAATTCATGAATCTTTCAACTAATTAAAAAATGACCAATCCTAACTAGTTGCAGAAG CTATTAATTAAATTTTTAAAAAAGTATATCTTTCTCTC TTATGAC TCACATAATTTATAKTC CC TATACT Gm08:836CAAAGTCTCACATAATTTATACTACAAAA[A/T]CT 8363193 3193 195 378 1 0.703TAGGTTTAATTTC GTACC TATTGTTAATGTTTC CTAATCGAAATTAGAATTTCACCCCGATAATTAAAA GTTTACATTAAAAAATTAYATAAATTACCGAAATAAAACTCAAAATTTAGTCAAACAATAATGTAAGC AC TAAGCAGCAAC TAAGAAGC TATAAACAAAGTTTTGATAAATAGTTAAATTTATC CTC CA AAGTGGGGAACTGTCGATCCATGGTGCTGGCAGCAACCGTAACATGCCAGGGTGCGAGATTTTCCGCA GTGGCTTCC GC GGGCCCACTGTTGCCAGCAGAGCAAACCACCACAAC GCCAC GC TTGGCCGCATGGAAGGATCC GATGGCAACACTATCCTTGAAAAAC GT Gm08:836GGAGGAAGAGCCACCGAGCGAGACGGAGAGG+A/ 3888 8363888 [A/G] 196 379 0.8250.809 G+ CATCGACGCCGTCGTGGATGGCGAGGTCGAAGGCCGCCAAGATATCAGCGTCGAAGCACTCCTCGC CTCCGACGGGGGGCCAGCAGACCTTGTAGGCTGCCACACGTGCCATTGGTGAGCCACCCTTGGCTGTTCCC TGGCCC TGGCC GAAGAC GC TGACAC GTGC GACCATGTTCCCGCCAGCTGTGGATAGGGTGTGG TGCCATTGGTGAGCCACCCTTGGCTGTTCCCTGGCCCTGGCCGAAGACGCTGACACGTGCGACCATGT TCCCGCCAGCTGTGGATAGGGTGTGGGTCCCGTGGCCCTCGTTGTCACGTGGCGAGTCAAAGGAGGA GTTCAGTGGGCCCGCCACTGAGGCGTAGCCCTTGGm08:836 TTGAAGTACCTTGCCCCTATTAGCTTCCTGC [A/G] 8364195 [A/G] 197 3800.919 0.788 4195 TTCAACATCTCCACTTAACGTTTCTTTAATTTWTCAAAACAAAATCATTGAAAGATTGGTCTGGTTGGT GTGAAAACACTAGTACTATAAAAGAATAAGATAAC GAAAGAAACATGTC TGC GTTCAAAGGAGTGC TTAACCCTTTCATTGTAGTATTCACCTAATAAAGAGTGCCAATTTAAAGGCATATGACTACAGAA R = Resistan; S = Susceptible *Liu etal. (2012). A soybean cyst nematode resistance gene points to a newmechanism of plant resistance to pathogens. Nature 492: 256-260.

TABLE 4 Non-limiting Examples of Amplicons Comprising the Various Marker LociProvided Herein. Resistant Linkage (R) or Marker Group Susceptible SEQAmplicon Name (ch) Primer 1 Primer 2 (S) Allele ID NO Amplicon SequenceSize (bp) S07160-1 A2 136868 136869 R 11 TGTGTTGTGTTTGACTG 118 (Gm08)CCATAACATGATGTTTG GATTAAATATAAACAA TAATATC C TATGCAGTT AGTGAGGCTGTGATTTGGAAGACACTGTCTTA TCAAGAGGCTTGGGAA ATG S07160-1 A2 136868 136869 S 12TGTGTTGTGTTTGACTG 118 (Gm08) CCATAACATGATGTTTG GATTAAATATAAACAA TAATATCA TATGCAGTT AGTGAGGCTGTGATTT GGAAGACACTGTCTTA TCAAGAGGCTTGGGAA ATG

In another embodiment, the method of detecting comprises DNA sequencingof at least one of the marker loci provided herein. As used herein,“sequencing” refers to sequencing methods for determining the order ofnucleotides in a molecule of DNA. Any DNA sequencing method known in theart can be used in the methods provided herein. Non-limiting examples ofDNA sequencing methods useful in the methods provided herein includeNext Generation Sequencing (NGS) technologies, for example, as describedin Egan, A. N, et al. (2012) American Journal of Botany 99(2):175-185;genotyping by sequencing (GBS) methods, for example, as described inElshire, R. J., et al. (2011) PLoS ONE 6(5):e19379; Molecular InversionProbe (MIP) genotyping, as described, for example, in Hardenbol, P., etal. (2003) Nature Biotechnology 21(6):673-678; or high throughputgenotyping by whole-genome resequencing, as described, for example inHuang, X et al., (2009) Genome Research 19:1068-1076. Each of the abovereferences is incorporated by reference in their entirety herein.

An active variant of any one of SEQ ID NOS: 1-380 can comprise apolynucleotide having at least 75%, 80% 85%, 90%, 91%, 92%, 93%, 94%,95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NOS: 1-380 as longas it is capable of amplifying and/or detecting the marker locus ofinterest. By “fragment” is intended a portion of the polynucleotide. Afragment or portion can comprise at least 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 50, 75, 100, 150, 200, 250, 300,350, 400 contiguous nucleotides of SEQ ID NOS: 1-380 as long as it iscapable of amplifying and/or detecting the marker locus of interest.

Unless otherwise stated, sequence identity/similarity values providedherein refer to the value obtained using GAP Version 10 using thefollowing parameters: % identity and % similarity for a nucleotidesequence using GAP Weight of 50 and Length Weight of 3, and thenwsgapdna.cmp scoring matrix; or any equivalent program thereof. By“equivalent program” is intended any sequence comparison program that,for any two sequences in question, generates an alignment havingidentical nucleotide residue matches and an identical percent sequenceidentity when compared to the corresponding alignment generated by GAPVersion 10.

Traits or markers are considered to be linked if they co-segregate. A1/100 probability of recombination per generation is defined as a mapdistance of 1.0 centiMorgan (1.0 cM). Genetic elements or genes locatedon a single chromosome segment are physically linked. Two loci can belocated in close proximity such that recombination between homologouschromosome pairs does not occur between the two loci during meiosis withhigh frequency, e.g., such that linked loci co-segregate at least about90% of the time, e.g., 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%,99.5%, 99.75%, or more of the time. Genetic elements located within achromosome segment are also genetically linked, typically within agenetic recombination distance of less than or equal to 50 centimorgans(cM), e.g., about 49, 40, 30, 20, 10, 5, 4, 3, 2, 1, 0.75, 0.5, or 0.25cM or less. That is, two genetic elements within a single chromosomesegment undergo recombination during meiosis with each other at afrequency of less than or equal to about 50%, e.g., about 49%, 40%, 30%,20%, 10%, 5%, 4%, 3%, 2%, 1%, 0.75%, 0.5%, or 0.25% or less. Closelylinked markers display a cross over frequency with a given marker ofabout 10% or less (the given marker is within about 10 cM of a closelylinked marker). In specific embodiments, a closely linked marker iswithin 10 cM, 9 cM, 8 cM, 7 cM, 6 cM, 5 cM, 4 cM, 3 cM, 2 cM or 1 cM ofany given marker disclosed herein. In further embodiments, a markerassociated with one of the markers disclosed herein can be within 75 Kb,60 Kb, 50 Kb, 40 Kb, 30 Kb, 20 K, 10 Kb, 5 Kb or less of the disclosedmarker.

Put another way, closely linked loci co-segregate at least about 90% ofthe time. Genetic linkage as evaluated by recombination frequency isimpacted by the chromatin structure of the region comprising the loci.Typically, the region is assumed to have a euchromatin structure duringinitial evaluations. However, some regions, such are regions closer tocentrosomes, have a heterochromatin structure. Without furtherinformation, the predicted physical distance between genetic mappositions is based on the assumption that the region is euchromatic,however if the region comprises heterochromatin the markers may bephysically closer together. With regard to physical position on achromosome, closely linked markers can be separated, for example, byabout 1 megabase (Mb; 1 million nucleotides), about 500 kilobases (Kb;1000 nucleotides), about 400 Kb, about 300 Kb, about 200 Kb, about 100Kb, about 50 Kb, about 25 Kb, about 10 Kb, about 5 Kb, about 2 Kb, about1 Kb, about 500 nucleotides, about 250 nucleotides, or less.

When referring to the relationship between two genetic elements, such asa genetic element contributing to resistance and a proximal marker,“coupling” phase linkage indicates the state where the “favorable”allele at the resistance locus is physically associated on the samechromosome strand as the “favorable” allele of the respective linkedmarker locus. In coupling phase, both favorable alleles are inheritedtogether by progeny that inherit that chromosome strand. In “repulsion”phase linkage, the “favorable” allele at the locus of interest (e.g., aQTL for resistance) is physically linked with an “unfavorable” allele atthe proximal marker locus, and the two “favorable” alleles are notinherited together (i.e., the two loci are “out of phase” with eachother).

Markers are used to define a specific locus on the soybean genome. Eachmarker is therefore an indicator of a specific segment of DNA, having aunique nucleotide sequence. Map positions provide a measure of therelative positions of particular markers with respect to one another.When a trait is stated to be linked to a given marker it will beunderstood that the actual DNA segment whose sequence affects the traitgenerally co-segregates with the marker. More precise and definitelocalization of a trait can be obtained if markers are identified onboth sides of the trait. By measuring the appearance of the marker(s) inprogeny of crosses, the existence of the trait can be detected byrelatively simple molecular tests without actually evaluating theappearance of the trait itself, which can be difficult andtime-consuming because the actual evaluation of the trait requiresgrowing plants to a stage and/or under environmental conditions wherethe trait can be expressed. Molecular markers have been widely used todetermine genetic composition in soybeans.

Favorable genotypes associated with at least trait of interest may beidentified by one or more methodologies. In some examples one or moremarkers are used, including but not limited to AFLPs, RFLPs, ASH, SSRs,SNPs, indels, padlock probes, molecular inversion probes, microarrays,sequencing, and the like. In some methods, a target nucleic acid isamplified prior to hybridization with a probe. In other cases, thetarget nucleic acid is not amplified prior to hybridization, such asmethods using molecular inversion probes (see, for example Hardenbol etal. (2003) Nat Biotech 21:673-678). In some examples, the genotyperelated to a specific trait is monitored, while in other examples, agenome-wide evaluation including but not limited to one or more ofmarker panels, library screens, association studies, microarrays, genechips, expression studies, or sequencing such as whole-genomeresequencing and genotyping-by-sequencing (GBS) may be used. In someexamples, no target-specific probe is needed, for example by usingsequencing technologies, including but not limited to next-generationsequencing methods (see, for example, Metzker (2010) Nat Rev Genet11:31-46; and, Egan et al. (2012) Am J Bot 99:175-185) such assequencing by synthesis (e.g., Roche 454 pyrosequencing, Illumina GenomeAnalyzer, and Ion Torrent PGM or Proton systems), sequencing by ligation(e.g., SOLiD from Applied Biosystems, and Polnator system from AzcoBiotech), and single molecule sequencing (SMS or third-generationsequencing) which eliminate template amplification (e.g., Helicossystem, and PacBio RS system from Pacific BioSciences). Furthertechnologies include optical sequencing systems (e.g., Starlight fromLife Technologies), and nanopore sequencing (e.g., GridION from OxfordNanopore Technologies). Each of these may be coupled with one or moreenrichment strategies for organellar or nuclear genomes in order toreduce the complexity of the genome under investigation via PCR,hybridization, restriction enzyme (see, e.g., Elshire et al. (2011) PLoSONE 6:e19379), and expression methods. In some examples, no referencegenome sequence is needed in order to complete the analysis.

The use of marker assisted selection (MAS) to select a soybean plant orgermplasm which has a certain marker locus, haplotype or marker profileis provided. For instance, in certain examples a soybean plant orgermplasm possessing a certain predetermined favorable marker locus orhaplotype will be selected via MAS. In certain other examples, a soybeanplant or germplasm possessing a certain predetermined favorable markerprofile will be selected via MAS.

Using MAS, soybean plants or germplasm can be selected for markers ormarker alleles that positively correlate with soybean cyst nematoderesistance, without actually raising soybean and measuring forresistance (or, contrawise, soybean plants can be selected against ifthey possess markers that negatively correlate with resistance). MAS isa powerful tool to select for desired phenotypes and for introgressingdesired traits into cultivars of soybean (e.g., introgressing desiredtraits into elite lines). MAS is easily adapted to high throughputmolecular analysis methods that can quickly screen large numbers ofplant or germplasm genetic material for the markers of interest and ismuch more cost effective than raising and observing plants for visibletraits.

In some embodiments, the molecular markers or marker loci are detectedusing a suitable amplification-based detection method. In these types ofmethods, nucleic acid primers are typically hybridized to the conservedregions flanking the polymorphic marker region. In certain methods,nucleic acid probes that bind to the amplified region are also employed.In general, synthetic methods for making oligonucleotides, includingprimers and probes, are well known in the art. For example,oligonucleotides can be synthesized chemically according to the solidphase phosphoramidite triester method described by Beaucage andCaruthers (1981) Tetrahedron Letts 22:1859-1862, e.g., using acommercially available automated synthesizer, e.g., as described inNeedham-VanDevanter, et al. (1984) Nucleic Acids Res. 12:6159-6168.Oligonucleotides, including modified oligonucleotides, can also beordered from a variety of commercial sources known to persons of skillin the art.

It will be appreciated that suitable primers and probes to be used canbe designed using any suitable method. It is not intended that theinvention be limited to any particular primer, primer pair or probe. Forexample, primers can be designed using any suitable software program,such as LASERGENE® or Primer3.

It is not intended that the primers be limited to generating an ampliconof any particular size. For example, the primers used to amplify themarker loci and alleles herein are not limited to amplifying the entireregion of the relevant locus. In some embodiments, marker amplificationproduces an amplicon at least 20 nucleotides in length, oralternatively, at least 50 nucleotides in length, or alternatively, atleast 100 nucleotides in length, or alternatively, at least 200nucleotides in length.

Non-limiting examples of polynucleotide primers useful for detecting themarker loci provided herein are provided in Table 1 and include, forexample, SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8 or variants or fragmentsthereof.

PCR, RT-PCR, and LCR are in particularly broad use as amplification andamplification-detection methods for amplifying nucleic acids of interest(e.g., those comprising marker loci), facilitating detection of themarkers. Details regarding the use of these and other amplificationmethods are well known in the art and can be found in any of a varietyof standard texts. Details for these techniques can also be found innumerous journal and patent references, such as Mullis, et al. (1987)U.S. Pat. No. 4,683,202; Arnheim & Levinson (Oct. 1, 1990) C&EN 36-47;Kwoh, et al. (1989) Proc. Natl. Acad. Sci. USA 86:1173; Guatelli, etal., (1990) Proc. Natl. Acad. Sci. USA 87:1874; Lomell, et al., (1989)J. Clin. Chem. 35:1826; Landegren, et al., (1988) Science 241:1077-1080;Van Brunt, (1990) Biotechnology 8:291-294; Wu and Wallace, (1989) Gene4:560; Barringer, et al., (1990) Gene 89:117, and Sooknanan and Malek,(1995) Biotechnology 13:563-564.

Such nucleic acid amplification techniques can be applied to amplifyand/or detect nucleic acids of interest, such as nucleic acidscomprising marker loci. Amplification primers for amplifying usefulmarker loci and suitable probes to detect useful marker loci or togenotype SNP alleles are provided. For example, exemplary primers andprobes are provided in SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 and inTables 1 and 2, and the genomic loci comprising the various marker lociprovided herein are provided in SEQ ID NOS: 13, 14, 15, 16, 17, 18, 19,20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37,38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55,56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73,74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91,92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107,108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121,122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135,136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149,150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163,164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177,178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191,192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205,206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219,220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233,234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247,248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261,262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275,276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289,290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303,304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317,318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331,332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345,346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359,360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373,374, 375, 376, 377, 378, 379, 380 and in Tables 3A and 3B. Non-limitingexamples of amplicon sequences comprising the marker loci providedherein are provided SEQ ID NOS: 11, 12 and in Table 4.

However, one of skill will immediately recognize that other primer andprobe sequences could also be used. For instance primers to either sideof the given primers can be used in place of the given primers, so longas the primers can amplify a region that includes the allele to bedetected, as can primers and probes directed to other SNP marker loci.Further, it will be appreciated that the precise probe to be used fordetection can vary, e.g., any probe that can identify the region of amarker amplicon to be detected can be substituted for those examplesprovided herein. Further, the configuration of the amplification primersand detection probes can, of course, vary. Thus, the compositions andmethods are not limited to the primers and probes specifically recitedherein.

In certain examples, probes will possess a detectable label. Anysuitable label can be used with a probe. Detectable labels suitable foruse with nucleic acid probes include, for example, any compositiondetectable by spectroscopic, radioisotopic, photochemical, biochemical,immunochemical, electrical, optical, or chemical means. Useful labelsinclude biotin for staining with labeled streptavidin conjugate,magnetic beads, fluorescent dyes, radiolabels, enzymes, and colorimetriclabels. Other labels include ligands, which bind to antibodies labeledwith fluorophores, chemiluminescent agents, and enzymes. A probe canalso constitute radiolabelled PCR primers that are used to generate aradiolabelled amplicon. Labeling strategies for labeling nucleic acidsand corresponding detection strategies can be found, e.g., in Haugland(1996) Handbook of Fluorescent Probes and Research Chemicals SixthEdition by Molecular Probes, Inc. (Eugene O R); or Haugland (2001)Handbook of Fluorescent Probes and Research Chemicals Eighth Edition byMolecular Probes, Inc. (Eugene O R).

Detectable labels may also include reporter-quencher pairs, such as areemployed in Molecular Beacon and TaqMan™ probes. The reporter may be afluorescent organic dye modified with a suitable linking group forattachment to the oligonucleotide, such as to the terminal 3′ carbon orterminal 5′ carbon. The quencher may also be an organic dye, which mayor may not be fluorescent, depending on the embodiment. Generally,whether the quencher is fluorescent or simply releases the transferredenergy from the reporter by non-radiative decay, the absorption band ofthe quencher should at least substantially overlap the fluorescentemission band of the reporter to optimize the quenching. Non-fluorescentquenchers or dark quenchers typically function by absorbing energy fromexcited reporters, but do not release the energy radiatively.

Selection of appropriate reporter-quencher pairs for particular probesmay be undertaken in accordance with known techniques. Fluorescent anddark quenchers and their relevant optical properties from whichexemplary reporter-quencher pairs may be selected are listed anddescribed, for example, in Berlman, Handbook of Fluorescence Spectra ofAromatic Molecules, 2nd ed., Academic Press, New York, 1971, the contentof which is incorporated herein by reference. Examples of modifyingreporters and quenchers for covalent attachment via common reactivegroups that can be added to an oligonucleotide in the present inventionmay be found, for example, in Haugland, Handbook of Fluorescent Probesand Research Chemicals, Molecular Probes of Eugene, Oreg., 1992, thecontent of which is incorporated herein by reference.

In certain examples, reporter-quencher pairs are selected from xanthenedyes including fluoresceins and rhodamine dyes. Many suitable forms ofthese compounds are available commercially with substituents on thephenyl groups, which can be used as the site for bonding or as thebonding functionality for attachment to an oligonucleotide. Anotheruseful group of fluorescent compounds for use as reporters are thenaphthylamines, having an amino group in the alpha or beta position.Included among such naphthylamino compounds are1-dimethylaminonaphthyl-5 sulfonate, 1-anilino-8-naphthalene sulfonateand 2-p-touidinyl-6-naphthalene sulfonate. Other dyes include3-phenyl-7-isocyanatocoumarin; acridines such as9-isothiocyanatoacridine; N-(p-(2-benzoxazolyl)phenyl)maleimide;benzoxadiazoles; stilbenes; pyrenes and the like. In certain otherexamples, the reporters and quenchers are selected from fluorescein andrhodamine dyes. These dyes and appropriate linking methodologies forattachment to oligonucleotides are well known in the art.

Suitable examples of reporters may be selected from dyes such as SYBRgreen, 5-carboxyfluorescein (5-FAM™ available from Applied Biosystems ofFoster City, Calif.), 6-carboxyfluorescein (6-FAM),tetrachloro-6-carboxyfluorescein (TET),2,7-dimethoxy-4,5-dichloro-6-carboxyfluorescein,hexachloro-6-carboxyfluorescein (HEX),6-carboxy-2′,4,7,7′-tetrachlorofluorescein (6-TET™ available fromApplied Biosystems), carboxy-X-rhodamine (ROX),6-carboxy-4′,5′-dichloro-2′,7′-dimethoxyfluorescein (6-JOE™ availablefrom Applied Biosystems), VIC™ dye products available from MolecularProbes, Inc., NED™ dye products available from Applied Biosystems, andthe like. Suitable examples of quenchers may be selected from6-carboxy-tetramethyl-rhodamine, 4-(4-dimethylaminophenylazo) benzoicacid (DABYL), tetramethylrhodamine (TAMRA), BHQ-0™, BHQ-1™, BHQ-2™, andBHQ-3™, each of which are available from Biosearch Technologies, Inc. ofNovato, Calif., QSY-7™, QSY-9™, QSY-21™ and QSY-35™, each of which areavailable from Molecular Probes, Inc., and the like.

In one aspect, real time PCR or LCR is performed on the amplificationmixtures described herein, e.g., using molecular beacons or TaqMan™probes. A molecular beacon (MB) is an oligonucleotide which, underappropriate hybridization conditions, self-hybridizes to form a stem andloop structure. The MB has a label and a quencher at the termini of theoligonucleotide; thus, under conditions that permit intra-molecularhybridization, the label is typically quenched (or at least altered inits fluorescence) by the quencher. Under conditions where the MB doesnot display intra-molecular hybridization (e.g., when bound to a targetnucleic acid, such as to a region of an amplicon during amplification),the MB label is unquenched. Details regarding standard methods of makingand using MBs are well established in the literature and MBs areavailable from a number of commercial reagent sources. See also, e.g.,Leone, et al., (1995) Molecular beacon probes combined withamplification by NASBA enable homogenous real-time detection of RNA,Nucleic Acids Res. 26:2150-2155; Tyagi and Kramer, (1996) Molecularbeacons: probes that fluoresce upon hybridization, Nature Biotechnology14:303-308; Blok and Kramer, (1997) Amplifiable hybridization probescontaining a molecular switch, Mol Cell Probes 11:187-194; Hsuih. etal., (1997) Novel, ligation-dependent PCR assay for detection ofhepatitis C in serum, J Clin Microbiol 34:501-507; Kostrikis, et al.,(1998) Molecular beacons: spectral genotyping of human alleles, Science279:1228-1229; Sokol, et al., (1998) Real time detection of DNA:RNAhybridization in living cells, Proc. Natl. Acad. Sci. U.S.A.95:11538-11543; Tyagi, et al., (1998) Multicolor molecular beacons forallele discrimination, Nature Biotechnology 16:49-53; Bonnet, et al.,(1999) Thermodynamic basis of the chemical specificity of structured DNAprobes, Proc. Natl. Acad. Sci. U.S.A. 96:6171-6176; Fang, et al. (1999)Designing a novel molecular beacon for surface-immobilized DNAhybridization studies, J. Am. Chem. Soc. 121:2921-2922; Marras, et al.,(1999) Multiplex detection of single-nucleotide variation usingmolecular beacons, Genet. Anal. Biomol. Eng. 14:151-156; and Vet, etal., (1999) Multiplex detection of four pathogenic retroviruses usingmolecular beacons, Proc. Natl. Acad. Sci. U.S.A. 96:6394-6399.Additional details regarding MB construction and use is found in thepatent literature, e.g., U.S. Pat. Nos. 5,925,517; 6,150,097; and6,037,130.

Another real-time detection method is the 5′-exonuclease detectionmethod, also called the TaqMan™ assay, as set forth in U.S. Pat. Nos.5,804,375; 5,538,848; 5,487,972; and 5,210,015, each of which is herebyincorporated by reference in its entirety. In the TaqMan™ assay, amodified probe, typically 10-25 nucleic acids in length, is employedduring PCR which binds intermediate to or between the two members of theamplification primer pair. The modified probe possesses a reporter and aquencher and is designed to generate a detectable signal to indicatethat it has hybridized with the target nucleic acid sequence during PCR.As long as both the reporter and the quencher are on the probe, thequencher stops the reporter from emitting a detectable signal. However,as the polymerase extends the primer during amplification, the intrinsic5′ to 3′ nuclease activity of the polymerase degrades the probe,separating the reporter from the quencher, and enabling the detectablesignal to be emitted. Generally, the amount of detectable signalgenerated during the amplification cycle is proportional to the amountof product generated in each cycle.

It is well known that the efficiency of quenching is a strong functionof the proximity of the reporter and the quencher, i.e., as the twomolecules get closer, the quenching efficiency increases. As quenchingis strongly dependent on the physical proximity of the reporter andquencher, the reporter and the quencher are preferably attached to theprobe within a few nucleotides of one another, usually within 30nucleotides of one another, more preferably with a separation of fromabout 6 to 16 nucleotides. Typically, this separation is achieved byattaching one member of a reporter-quencher pair to the 5′ end of theprobe and the other member to a nucleotide about 6 to 16 nucleotidesaway, in some cases at the 3′ end of the probe.

Separate detection probes can also be omitted in amplification/detectionmethods, e.g., by performing a real time amplification reaction thatdetects product formation by modification of the relevant amplificationprimer upon incorporation into a product, incorporation of labelednucleotides into an amplicon, or by monitoring changes in molecularrotation properties of amplicons as compared to unamplified precursors(e.g., by fluorescence polarization).

Further, it will be appreciated that amplification is not a requirementfor marker detection—for example, one can directly detect unamplifiedgenomic DNA simply by performing a Southern blot on a sample of genomicDNA. Procedures for performing Southern blotting, amplification e.g.,(PCR, LCR, or the like), and many other nucleic acid detection methodsare well established and are taught, e.g., in Sambrook, et al.,Molecular Cloning—A Laboratory Manual (3d ed.), Vol. 1-3, Cold SpringHarbor Laboratory, Cold Spring Harbor, N.Y., 2000 (“Sambrook”); CurrentProtocols in Molecular Biology, F. M. Ausubel, et al., eds., CurrentProtocols, a joint venture between Greene Publishing Associates, Inc.and John Wiley & Sons, Inc., (supplemented through 2002) (“Ausubel”))and PCR Protocols A Guide to Methods and Applications (Innis, et al.,eds) Academic Press Inc. San Diego, Calif. (1990) (Innis). Additionaldetails regarding detection of nucleic acids in plants can also befound, e.g., in Plant Molecular Biology (1993) Croy (ed.) BIOSScientific Publishers, Inc.

Other techniques for detecting SNPs can also be employed, such as allelespecific hybridization (ASH). ASH technology is based on the stableannealing of a short, single-stranded, oligonucleotide probe to acompletely complementary single-stranded target nucleic acid. Detectionis via an isotopic or non-isotopic label attached to the probe. For eachpolymorphism, two or more different ASH probes are designed to haveidentical DNA sequences except at the polymorphic nucleotides. Eachprobe will have exact homology with one allele sequence so that therange of probes can distinguish all the known alternative allelesequences. Each probe is hybridized to the target DNA. With appropriateprobe design and hybridization conditions, a single-base mismatchbetween the probe and target DNA will prevent hybridization.

Real-time amplification assays, including MB or TaqMan™ based assays,are especially useful for detecting SNP alleles. In such cases, probesare typically designed to bind to the amplicon region that includes theSNP locus, with one allele-specific probe being designed for eachpossible SNP allele. For instance, if there are two known SNP allelesfor a particular SNP locus, “A” or “C,” then one probe is designed withan “A” at the SNP position, while a separate probe is designed with a“C” at the SNP position. While the probes are typically identical to oneanother other than at the SNP position, they need not be. For instance,the two allele-specific probes could be shifted upstream or downstreamrelative to one another by one or more bases. However, if the probes arenot otherwise identical, they should be designed such that they bindwith approximately equal efficiencies, which can be accomplished bydesigning under a strict set of parameters that restrict the chemicalproperties of the probes. Further, a different detectable label, forinstance a different reporter-quencher pair, is typically employed oneach different allele-specific probe to permit differential detection ofeach probe. In certain examples, each allele-specific probe for acertain SNP locus is 11-20 nucleotides in length, dual-labeled with aflorescence quencher at the 3′ end and either the 6-FAM(6-carboxyfluorescein) or VIC(4,7,2′-trichloro-7′-phenyl-6-carboxyfluorescein) fluorophore at the 5′end.

To effectuate SNP allele detection, a real-time PCR reaction can beperformed using primers that amplify the region including the SNP locus,for instance the sequences listed in Tables 3A and 3B, the reactionbeing performed in the presence of all allele-specific probes for thegiven SNP locus. By then detecting signal for each detectable labelemployed and determining which detectable label(s) demonstrated anincreased signal, a determination can be made of which allele-specificprobe(s) bound to the amplicon and, thus, which SNP allele(s) theamplicon possessed. For instance, when 6-FAM- and VIC-labeled probes areemployed, the distinct emission wavelengths of 6-FAM (518 nm) and VIC(554 nm) can be captured. A sample that is homozygous for one allelewill have fluorescence from only the respective 6-FAM or VICfluorophore, while a sample that is heterozygous at the analyzed locuswill have both 6-FAM and VIC fluorescence.

The KASPar® and Illumina® Detection Systems are additional examples ofcommercially-available marker detection systems. KASPar® is ahomogeneous fluorescent genotyping system which utilizes allele specifichybridization and a unique form of allele specific PCR (primerextension) in order to identify genetic markers (e.g. a particular SNPlocus associated with soybean cyst nematode resistance). Illumina®detection systems utilize similar technology in a fixed platform format.The fixed platform utilizes a physical plate that can be created with upto 384 markers. The Illumina® system is created with a single set ofmarkers that cannot be changed and utilizes dyes to indicate markerdetection.

These systems and methods represent a wide variety of availabledetection methods which can be utilized to detect markers associatedwith resistance or improved resistance to soybean cyst nematode, but anyother suitable method could also be used.

Introgression of soybean cyst nematode resistance into non-resistant orless-resistant soybean germplasm is provided. Any method forintrogressing one or more marker loci into soybean plants known to oneof skill in the art can be used. Typically, a first soybean germplasmthat contains soybean cyst nematode resistance derived from a particularmarker locus, haplotype or marker profile and a second soybean germplasmthat lacks such resistance derived from the marker locus, haplotype ormarker profile are provided. The first soybean germplasm may be crossedwith the second soybean germplasm to provide progeny soybean germplasm.These progeny germplasm are screened to determine the presence ofsoybean cyst nematode resistance derived from the marker locus,haplotype or marker profile, and progeny that tests positive for thepresence of resistance derived from the marker locus, haplotype ormarker profile are selected as being soybean germplasm into which themarker locus, haplotype or marker profile has been introgressed. Methodsfor performing such screening are well known in the art and any suitablemethod can be used.

One application of MAS is to use the resistance markers, haplotypes ormarker profiles to increase the efficiency of an introgression orbackcrossing effort aimed at introducing a resistance trait into adesired (typically high yielding) background. In marker assistedbackcrossing of specific markers from a donor source, e.g., to an elitegenetic background, one selects among backcross progeny for the donortrait and then uses repeated backcrossing to the elite line toreconstitute as much of the elite background's genome as possible.

Thus, the markers and methods can be utilized to guide marker assistedselection or breeding of soybean varieties with the desired complement(set) of allelic forms of chromosome segments associated with superioragronomic performance (resistance, along with any other availablemarkers for yield, disease tolerance, etc.). Any of the disclosed markerloci, marker alleles, haplotypes, or marker profiles can be introducedinto a soybean line via introgression, by traditional breeding (orintroduced via transformation, or both) to yield a soybean plant withsuperior agronomic performance. The number of alleles associated withresistance that can be introduced or be present in a soybean plantranges from 1 to the number of alleles disclosed herein, each integer ofwhich is incorporated herein as if explicitly recited.

The markers and methods provided herein can also be utilized to guidemarker assisted selection or breeding of soybean varieties comprisingother soybean cyst nematode resistance markers or alleles to create amolecular stack for soybean cyst nematode resistance. For example, anyof the marker loci provided herein can be introduced into a soybean linehaving one or more of the soybean cyst nematode resistance loci rhg1,rhg2, rhg3 or rhg5. In one embodiment, any one or more of the markerloci provided herein can be stacked with the rhg1 locus. In anotherembodiment, any one or more of the marker loci provided herein can bestacked with the rhg2 locus. In a further embodiment, any one or more ofthe marker loci provided herein can be stacked with the rhg1 and rhg2loci.

This also provides a method of making a progeny soybean plant and theseprogeny soybean plants, per se. The method comprises crossing a firstparent soybean plant with a second soybean plant and growing the femalesoybean plant under plant growth conditions to yield soybean plantprogeny. Methods of crossing and growing soybean plants are well withinthe ability of those of ordinary skill in the art. Such soybean plantprogeny can be assayed for alleles associated with resistance and,thereby, the desired progeny selected. Such progeny plants or seed canbe sold commercially for soybean production, used for food, processed toobtain a desired constituent of the soybean, or further utilized insubsequent rounds of breeding. At least one of the first or secondsoybean plants is a soybean plant in that it comprises at least one ofthe marker loci or marker profiles, such that the progeny are capable ofinheriting the marker locus or marker profile.

Often, a method is applied to at least one related soybean plant such asfrom progenitor or descendant lines in the subject soybean plantspedigree such that inheritance of the desired resistance can be traced.The number of generations separating the soybean plants being subject tothe methods provided herein will generally be from 1 to 20, commonly 1to 5, and typically 1, 2, or 3 generations of separation, and quiteoften a direct descendant or parent of the soybean plant will be subjectto the method (i.e., 1 generation of separation).

Genetic diversity is important for long term genetic gain in anybreeding program. With limited diversity, genetic gain will eventuallyplateau when all of the favorable alleles have been fixed within theelite population. One objective is to incorporate diversity into anelite pool without losing the genetic gain that has already been madeand with the minimum possible investment. MAS provides an indication ofwhich genomic regions and which favorable alleles from the originalancestors have been selected for and conserved over time, facilitatingefforts to incorporate favorable variation from exotic germplasm sources(parents that are unrelated to the elite gene pool) in the hopes offinding favorable alleles that do not currently exist in the elite genepool.

For example, the markers, haplotypes, primers, probes, and markerprofiles can be used for MAS in crosses involving elite x exotic soybeanlines by subjecting the segregating progeny to MAS to maintain majoryield alleles, along with the resistance marker alleles herein.

As an alternative to standard breeding methods of introducing traits ofinterest into soybean (e.g., introgression), transgenic approaches canalso be used to create transgenic plants with the desired traits. Inthese methods, exogenous nucleic acids that encode a desired markerloci, marker profile or haplotype are introduced into target plants orgermplasm. For example, a nucleic acid that codes for a resistance traitis cloned, e.g., via positional cloning, and introduced into a targetplant or germplasm.

Experienced plant breeders can recognize resistant soybean plants in thefield, and can select the resistant individuals or populations forbreeding purposes or for propagation. In this context, the plant breederrecognizes “resistant” and “non-resistant” or “susceptible” soybeanplants. However, plant resistance is a phenotypic spectrum consisting ofextremes in resistance and susceptibility, as well as a continuum ofintermediate resistance phenotypes. Evaluation of these intermediatephenotypes using reproducible assays are of value to scientists who seekto identify genetic loci that impart resistance, to conduct markerassisted selection for resistant populations, and to use introgressiontechniques to breed a resistance trait into an elite soybean line, forexample.

By “improved resistance” is intended that the plants show a decrease inthe disease symptoms that are the outcome of plant exposure to soybeancyst nematode. That is, the damage caused by soybean cyst nematode isprevented, or alternatively, the disease symptoms caused by soybean cystnematode is minimized or lessened. Thus, improved resistance to soybeancyst nematode can result in reduction of the disease symptoms by atleast about 2% to at least about 6%, at least about 5% to about 50%, atleast about 10% to about 60%, at least about 30% to about 70%, at leastabout 40% to about 80%, or at least about 50% to about 90% or greater.Hence, the methods provided herein can be utilized to protect plantsfrom soybean cyst nematode.

Screening and selection of soybean cyst nematode resistant soybeanplants may be performed, for example, by exposing plants to soybean cystnematode and selecting those plants showing resistance to soybean cystnematode. Various assays can be used to measure resistance or improvedresistance to soybean cyst nematode. For example, soybean cyst nematoderesistance can be determined by visual observations after plant exposureto a particular race of soybean cyst nematode, such as race 1, 2, 3, 5or 14. Scores range from 1 to 9 and indicate visual observations ofresistance as compared to other genotypes in the test. A score of 1indicates soybean cyst nematode are able to infect the plant and causeyield loss, while a score of 9 indicates soybean cyst nematoderesistance. Preliminary scores are reported as double digits, forexample, ‘55’ indicates a preliminary score of 5 on the scale of 1 to 9.

Non-limiting examples of soybean cyst nematode resistance phenotypicscreening are described in detail below.

Multiple populations of Heterodera glycines are maintained and increasedon host plants. These populations are used to identify, purify, andcharacterize elite soybean varieties for resistance to soybean cystnematode. The following races of soybean cyst nematode are maintained:Race 1 (Type HG 2.5), Race 2 (Type HG 1.2.5.7), Race 3 (Type HG 0 orType HG 7), Race 5 (Type HG 2.5.7), and Race 14 (Type HG 1.3.6.7).

Eggs or second stage juveniles (J2) are used to inoculate host plants toincrease their population. Soybean cyst nematode infestation requires aminimum 35 days before the cysts reach maturity and can be used toinoculate soybean experiments. Cyst eggs/J2 inoculant is harvestedthrough a series of washings, grindings, and screenings. Screens areused progressing from larger to smaller sizes, ending with a #500 (25μm) screen.

Soybean plants are grown in cones. Cones are long containersapproximately 12 inches long and 1.5 inches in diameter at the top(e.g., Ray Leach Cone-tainers™). The cone is designed to easily removethe root mass. Three to seven days after planting, an inoculum channelis made in the cone containing the experimental line by poking a 4 inchhole with a 10 ml pipette tip. One ml of inoculum is dispensed into thechannel. The plants are watered manually for the duration of the test,with watering being moderately light during the first 3-5 days until J2infects the roots.

Plants are scored approximately 28-35 days following inoculation whencyst reproduction on susceptible checks is sufficiently high. Plants areremoved from their cones and the soil is removed from the roots bygently dipping the roots into a bucket of water. The plants are screenedto identify native resistance to one or more of the five races ofsoybean cyst nematode inoculated using a combination of three methods(1) visual 9-6-1 score; (2) visual full count; and/or (3) microscopecount score depending on the stage of the line when screened. Ingeneral, lines earlier in the development cycle (R1-R2) are screened bythe visual 9-6-1 method, and lines that have progressed to laterdevelopment phases (R3-R5) are screened by the visual full count and/ormicroscope count method(s).

One typical phenotyping method is a visual evaluation of the roots.Susceptible checks are first evaluated for the development of cysts onthe root system. These counts are recorded and averaged across theexperiment to determine the susceptible (SUS) check average. Roots fromthe test plants are then scored based on a comparison with the averageof the susceptible checks as follows:

9=0-15% of the susceptible checks average

6=16-40% of the susceptible checks average

1=≧41% of the susceptible checks average

Visual counts: In this method, known checks are counted and reported infull. Observed cysts on the test plants are counted for comparison tothe susceptible check plant scores. Cyst counts are converted to 1-9scores based on the female index (FI). The female index (FI) is thepercentage of the number of females cysts produced on each experimentalline divided by the number produced on a standard susceptible soybeancheck, then the result is multiplied by 100. A low FI (<10) means thatthe soybean cyst nematode population is not able to reproduce well onthe test line, a high FI means that the soybean cyst nematode populationis able to reproduce well on the test line.Microscope counts: Cysts counts for soybean cyst nematode assays forchecks and experimental line are determined by washing cysts from rootsand counting the number of cysts under the microscope.

At about 28-35 days after inoculation, roots from the susceptible checkcontrols are examined for yellow cysts to assess whether to begin theprocess of evaluating the test. Experimental lines are compared withknown standard checks. Once adequate levels of cysts are detected on thecheck varieties, plants from the test lines are removed from cones oneat a time. Soil is removed from roots by gently dipping the roots into abucket of water. The root tissue is placed on a 850 micron (#20) poresieve stacked over a 250 micron (#60) pore sieve and sprayed with a jetof water to dislodge cysts from the roots. Collected cysts are rinsedfrom the #60 sieve into a clean labeled cup using no more than 30 mls ofadditional water.

Once all the samples are collected, each sample is counted using agridded counting dish under a stereo microscope. The number of cystscounted are recorded for each sample. Cyst counts on the test plants areconverted to the 1-9 scoring scale based on the female index (FI)described above.

The following exemplary soybean cyst nematode checks, provided in Table5, can be planted and used to monitor cyst development:

TABLE 5 Exemplary soybean cyst nematode checks. Race 1 Race 2 Race 3Race 5 Race 14 92B12 RES 95M60 RES 9182 RES 92B12 RES 9182 RES 9281 SUS9281 SUS 9281 SUS 9281 SUS 9281 SUS 9234 RES PI437654 RES 9234 RES 9234RES 9234 SUS 9392 SUS 9392 SUS 9392 SUS 9392 SUS 9392 SUS 91M12 MR 9234MR 93B15 MR 91M12 SUS 93B15 MR RES = Resistant; SUS = Susceptible; and,MR = Moderately Resistant

In some examples, a kit or an automated system for detecting markerloci, haplotypes, and marker profiles, and/or correlating the markerloci, haplotypes, and marker profiles with a desired phenotype (e.g.,soybean cyst nematode resistance) are provided. As used herein, “kit”refers to a set of reagents for the purpose of performing the variousmethods of detecting or identifying herein, more particularly, theidentification and/or the detection of a soybean plant or germplasmhaving improved resistance to soybean cyst nematode.

In one embodiment, a kit for detecting or selecting at least one soybeanplant or soybean germplasm with resistance or improved resistance tosoybean cyst nematode is provided. Such a kit comprises (a) primers orprobes for detecting one or more marker loci associated with resistanceto soybean cyst nematode, wherein at least one of the primers and probesin the kit are capable of detecting a marker locus, wherein the markerlocus is associated with the rhg4 locus on linkage group A2; and (b)instructions for using the primers or probes for detecting the one ormore marker loci and correlating the detected marker loci with predictedresistance to soybean cyst nematode.

In a specific embodiment, the primers and probes of the kit are capableof detecting a marker locus comprising: (a) S07160-1 or a marker closelylinked thereto on linkage group A2; or (ii) a marker locus comprisingGm08:8300131, Gm08:8257778, Gm08:8257785, Gm08:8258163, Gm08:8258688,Gm08:8258742, Gm08:8259928, Gm08:8260451, Gm08:8260590, Gm08:8261480,Gm08:8261684, Gm08:8262165, Gm08:8263213, Gm08:8263250, Gm08:8263611,Gm08:8264149, Gm08:8265227, Gm08:8265364, Gm08:8265614, Gm08:8266183,Gm08:8266185, Gm08:8266263, Gm08:8266350, Gm08:8266386, Gm08:8266473,Gm08:8266888, Gm08:8267085, Gm08:8267166, Gm08:8267721, Gm08:8267826,Gm08:8268336, Gm08:8268861, Gm08:8269148, Gm08:8269785, Gm08:8270037,Gm08:8270562, Gm08:8270652, Gm08:8271540, Gm08:8271591, Gm08:8271649,Gm08:8271672, Gm08:8271955, Gm08:8273257, Gm08:8273355, Gm08:8273979,Gm08:8275766, Gm08:8275780, Gm08:8275959, Gm08:8276701, Gm08:8276849,Gm08:8276913, Gm08:8277162, Gm08:8277227, Gm08:8277248, Gm08:8277381,Gm08:8277383, Gm08:8277542, Gm08:8277625, Gm08:8277643, Gm08:8277876,Gm08:8277880, Gm08:8277969, Gm08:8278001, Gm08:8278167, Gm08:8278274,Gm08:8278434, Gm08:8279165, Gm08:8279230, Gm08:8279854, Gm08:8280901,Gm08:8280937, Gm08:8281564, Gm08:8282902, Gm08:8284027, Gm08:8286864,Gm08:8287265, Gm08:8287278, Gm08:8287453, Gm08:8287459, Gm08:8288039,Gm08:8288141, Gm08:8288200, Gm08:8288470, Gm08:8288831, Gm08:8289392,Gm08:8290740, Gm08:8291682, Gm08:8292207, Gm08:8297064, Gm08:8299433,Gm08:8299672, Gm08:8301839, Gm08:8302134, Gm08:8303450, Gm08:8305237,Gm08:8305348, Gm08:8305905, Gm08:8306090, Gm08:8306141, Gm08:8306210,Gm08:8306492, Gm08:8306627, Gm08:8307172, Gm08:8307665, Gm08:8308019,Gm08:8308891, Gm08:8308917, Gm08:8309316, Gm08:8309423, Gm08:8309837,Gm08:8310383, Gm08:8310464, Gm08:8310503, Gm08:8310663, Gm08:8311631,Gm08:8311906, Gm08:8312536, Gm08:8312819, Gm08:8313273, Gm08:8313923,Gm08:8314010, Gm08:8314025, Gm08:8314208, Gm08:8314292, Gm08:8314295,Gm08:8314513, Gm08:8314736, Gm08:8314791, Gm08:8314860, Gm08:8315543,Gm08:8315644, Gm08:8316113, Gm08:8316689, Gm08:8316899, Gm08:8317852,Gm08:8317861, Gm08:8318033, Gm08:8319087, Gm08:8319642, Gm08:8319647,Gm08:8320068, Gm08:8321253, Gm08:8321649, Gm08:8323937, Gm08:8324341,Gm08:8325127, Gm08:8325214, Gm08:8326696, Gm08:8326877, Gm08:8328633,Gm08:8330929, Gm08:8331132, Gm08:8331181, Gm08:8331408, Gm08:8331827,Gm08:8332651, Gm08:8332685, Gm08:8332957, Gm08:8343167, Gm08:8345187,Gm08:8345720, Gm08:8346030, Gm08:8346050, Gm08:8346352, Gm08:8346726,Gm08:8347799, Gm08:8348022, Gm08:8348028, Gm08:8349925, Gm08:8350122,Gm08:8350277, Gm08:8351061, Gm08:8351503, Gm08:8352313, Gm08:8352743,Gm08:8353341, Gm08:8355175, Gm08:8360133, Gm08:8363193, Gm08:8363888,Gm08:8364195 or a marker closely linked thereto.

Thus, a typical kit or system can include a set of marker probes orprimers configured to detect at least one favorable allele of one ormore marker loci associated with resistance to soybean cyst nematode,for instance a favorable marker locus, haplotype or marker profile.These probes or primers can be configured, for example, to detect themarker loci noted in the tables and examples herein, e.g., using anyavailable allele detection format, such as solid or liquid phase arraybased detection, microfluidic-based sample detection, etc. The systemsand kits can further include packaging materials for packaging theprobes, primers, or instructions, controls such as control amplificationreactions that include probes, primers or template nucleic acids foramplifications, molecular size markers, or the like.

A typical system can also include a detector that is configured todetect one or more signal outputs from the set of marker probes orprimers, or amplicon thereof, thereby identifying the presence orabsence of the allele. A wide variety of signal detection apparatus areavailable, including photo multiplier tubes, spectrophotometers, CCDarrays, scanning detectors, phototubes and photodiodes, microscopestations, galvo-scans, microfluidic nucleic acid amplification detectionappliances and the like. The precise configuration of the detector willdepend, in part, on the type of label used to detect the marker allele,as well as the instrumentation that is most conveniently obtained forthe user. Detectors that detect fluorescence, phosphorescence,radioactivity, pH, charge, absorbance, luminescence, temperature,magnetism or the like can be used. Typical detector examples includelight (e.g., fluorescence) detectors or radioactivity detectors. Forexample, detection of a light emission (e.g., a fluorescence emission)or other probe label is indicative of the presence or absence of amarker allele. Fluorescent detection is generally used for detection ofamplified nucleic acids (however, upstream and/or downstream operationscan also be performed on amplicons, which can involve other detectionmethods). In general, the detector detects one or more label (e.g.,light) emission from a probe label, which is indicative of the presenceor absence of a marker allele. The detector(s) optionally monitors oneor a plurality of signals from an amplification reaction. For example,the detector can monitor optical signals which correspond to “real time”amplification assay results.

System or kit instructions that describe how to use the system or kit orthat correlate the presence or absence of the favorable allele with thepredicted resistance are also provided. For example, the instructionscan include at least one look-up table that includes a correlationbetween the presence or absence of the favorable alleles, haplotypes, ormarker profiles and the predicted resistance. The precise form of theinstructions can vary depending on the components of the system, e.g.,they can be present as system software in one or more integrated unit ofthe system (e.g., a microprocessor, computer or computer readablemedium), or can be present in one or more units (e.g., computers orcomputer readable media) operably coupled to the detector. As noted, inone typical example, the system instructions include at least onelook-up table that includes a correlation between the presence orabsence of the favorable alleles and predicted resistance. Theinstructions also typically include instructions providing a userinterface with the system, e.g., to permit a user to view results of asample analysis and to input parameters into the system.

Isolated polynucleotides comprising the nucleic acid sequences of theprimers and probes provided herein are also encompassed herein. In oneembodiment, the isolated polynucleotide comprises a polynucleotidecapable of detecting a marker locus of the soybean genome comprising:(a) S07160-1, or a marker closely linked thereto on linkage group A2; or(b) Gm08:8300131, Gm08:8257778, Gm08:8257785, Gm08:8258163,Gm08:8258688, Gm08:8258742, Gm08:8259928, Gm08:8260451, Gm08:8260590,Gm08:8261480, Gm08:8261684, Gm08:8262165, Gm08:8263213, Gm08:8263250,Gm08:8263611, Gm08:8264149, Gm08:8265227, Gm08:8265364, Gm08:8265614,Gm08:8266183, Gm08:8266185, Gm08:8266263, Gm08:8266350, Gm08:8266386,Gm08:8266473, Gm08:8266888, Gm08:8267085, Gm08:8267166, Gm08:8267721,Gm08:8267826, Gm08:8268336, Gm08:8268861, Gm08:8269148, Gm08:8269785,Gm08:8270037, Gm08:8270562, Gm08:8270652, Gm08:8271540, Gm08:8271591,Gm08:8271649, Gm08:8271672, Gm08:8271955, Gm08:8273257, Gm08:8273355,Gm08:8273979, Gm08:8275766, Gm08:8275780, Gm08:8275959, Gm08:8276701,Gm08:8276849, Gm08:8276913, Gm08:8277162, Gm08:8277227, Gm08:8277248,Gm08:8277381, Gm08:8277383, Gm08:8277542, Gm08:8277625, Gm08:8277643,Gm08:8277876, Gm08:8277880, Gm08:8277969, Gm08:8278001, Gm08:8278167,Gm08:8278274, Gm08:8278434, Gm08:8279165, Gm08:8279230, Gm08:8279854,Gm08:8280901, Gm08:8280937, Gm08:8281564, Gm08:8282902, Gm08:8284027,Gm08:8286864, Gm08:8287265, Gm08:8287278, Gm08:8287453, Gm08:8287459,Gm08:8288039, Gm08:8288141, Gm08:8288200, Gm08:8288470, Gm08:8288831,Gm08:8289392, Gm08:8290740, Gm08:8291682, Gm08:8292207, Gm08:8297064,Gm08:8299433, Gm08:8299672, Gm08:8301839, Gm08:8302134, Gm08:8303450,Gm08:8305237, Gm08:8305348, Gm08:8305905, Gm08:8306090, Gm08:8306141,Gm08:8306210, Gm08:8306492, Gm08:8306627, Gm08:8307172, Gm08:8307665,Gm08:8308019, Gm08:8308891, Gm08:8308917, Gm08:8309316, Gm08:8309423,Gm08:8309837, Gm08:8310383, Gm08:8310464, Gm08:8310503, Gm08:8310663,Gm08:8311631, Gm08:8311906, Gm08:8312536, Gm08:8312819, Gm08:8313273,Gm08:8313923, Gm08:8314010, Gm08:8314025, Gm08:8314208, Gm08:8314292,Gm08:8314295, Gm08:8314513, Gm08:8314736, Gm08:8314791, Gm08:8314860,Gm08:8315543, Gm08:8315644, Gm08:8316113, Gm08:8316689, Gm08:8316899,Gm08:8317852, Gm08:8317861, Gm08:8318033, Gm08:8319087, Gm08:8319642,Gm08:8319647, Gm08:8320068, Gm08:8321253, Gm08:8321649, Gm08:8323937,Gm08:8324341, Gm08:8325127, Gm08:8325214, Gm08:8326696, Gm08:8326877,Gm08:8328633, Gm08:8330929, Gm08:8331132, Gm08:8331181, Gm08:8331408,Gm08:8331827, Gm08:8332651, Gm08:8332685, Gm08:8332957, Gm08:8343167,Gm08:8345187, Gm08:8345720, Gm08:8346030, Gm08:8346050, Gm08:8346352,Gm08:8346726, Gm08:8347799, Gm08:8348022, Gm08:8348028, Gm08:8349925,Gm08:8350122, Gm08:8350277, Gm08:8351061, Gm08:8351503, Gm08:8352313,Gm08:8352743, Gm08:8353341, Gm08:8355175, Gm08:8360133, Gm08:8363193,Gm08:8363888, Gm08:8364195 or a marker closely linked thereto.

In specific embodiments, the isolated polynucleotide comprises: (a) apolynucleotide comprising SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10;(c) a polynucleotide having at least 90% sequence identity to SEQ IDNOs: 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10; or (d) a polynucleotide comprisingat least 10 contiguous nucleotides of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7,8, 9 or 10.

In certain embodiments, the isolated nucleic acids are capable ofhybridizing under stringent conditions to nucleic acids of a soybeancultivar resistant to soybean cyst nematode, for instance to particularSNPs that comprise a marker locus, haplotype or marker profile.

As used herein, a substantially identical or complementary sequence is apolynucleotide that will specifically hybridize to the complement of thenucleic acid molecule to which it is being compared under highstringency conditions. A polynucleotide is said to be the “complement”of another polynucleotide if they exhibit complementarity. As usedherein, molecules are said to exhibit “complete complementarity” whenevery nucleotide of one of the polynucleotide molecules is complementaryto a nucleotide of the other. Two molecules are said to be “minimallycomplementary” if they can hybridize to one another with sufficientstability to permit them to remain annealed to one another under atleast conventional “low-stringency” conditions. Similarly, the moleculesare said to be “complementary” if they can hybridize to one another withsufficient stability to permit them to remain annealed to one anotherunder conventional “high-stringency” conditions.

Appropriate stringency conditions which promote DNA hybridization, forexample, 6× sodium chloride/sodium citrate (SSC) at about 45° C.,followed by a wash of 2×SSC at 50° C., are known to those skilled in theart or can be found in Current Protocols in Molecular Biology, JohnWiley & Sons, N.Y. (1989), 6.3.1-6.3.6. Typically, stringent conditionsfor hybridization and detection will be those in which the saltconcentration is less than about 1.5 M Na ion, typically about 0.01 to1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3 and thetemperature is at least about 30° C. for short probes (e.g., 10 to 50nucleotides) and at least about 60° C. for long probes (e.g., greaterthan 50 nucleotides). Stringent conditions may also be achieved with theaddition of destabilizing agents such as formamide. Exemplary lowstringency conditions include hybridization with a buffer solution of 30to 35% formamide, 1 M NaCl, 1% SDS (sodium dodecyl sulphate) at 37° C.,and a wash in 1× to 2×SSC (20×SSC=3.0 M NaCl/0.3 M trisodium citrate) at50 to 55° C. Exemplary moderate stringency conditions includehybridization in 40 to 45% formamide, 1.0 M NaCl, 1% SDS at 37° C., anda wash in 0.5× to 1×SSC at 55 to 60° C. Exemplary high stringencyconditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at37° C., and a wash in 0.1×SSC at 60 to 65° C. Optionally, wash buffersmay comprise about 0.1% to about 1% SDS. Duration of hybridization isgenerally less than about 24 hours, usually about 4 to about 12 hours.The duration of the wash time will be at least a length of timesufficient to reach equilibrium.

Non-limiting examples of methods and compositions disclosed herein areas follows:

1. A method of identifying a first soybean plant or a first soybeangermplasm that displays resistance or improved resistance to soybeancyst nematode, the method comprising detecting in the genome of saidfirst soybean plant or in the genome of said first soybean germplasm atleast one marker locus that is associated with the resistance, whereinthe at least one marker locus comprises (a) S07160-1 or a marker closelylinked thereto on linkage group A2; or (b) Gm08:8300131, Gm08:8257778,Gm08:8257785, Gm08:8258163, Gm08:8258688, Gm08:8258742, Gm08:8259928,Gm08:8260451, Gm08:8260590, Gm08:8261480, Gm08:8261684, Gm08:8262165,Gm08:8263213, Gm08:8263250, Gm08:8263611, Gm08:8264149, Gm08:8265227,Gm08:8265364, Gm08:8265614, Gm08:8266183, Gm08:8266185, Gm08:8266263,Gm08:8266350, Gm08:8266386, Gm08:8266473, Gm08:8266888, Gm08:8267085,Gm08:8267166, Gm08:8267721, Gm08:8267826, Gm08:8268336, Gm08:8268861,Gm08:8269148, Gm08:8269785, Gm08:8270037, Gm08:8270562, Gm08:8270652,Gm08:8271540, Gm08:8271591, Gm08:8271649, Gm08:8271672, Gm08:8271955,Gm08:8273257, Gm08:8273355, Gm08:8273979, Gm08:8275766, Gm08:8275780,Gm08:8275959, Gm08:8276701, Gm08:8276849, Gm08:8276913, Gm08:8277162,Gm08:8277227, Gm08:8277248, Gm08:8277381, Gm08:8277383, Gm08:8277542,Gm08:8277625, Gm08:8277643, Gm08:8277876, Gm08:8277880, Gm08:8277969,Gm08:8278001, Gm08:8278167, Gm08:8278274, Gm08:8278434, Gm08:8279165,Gm08:8279230, Gm08:8279854, Gm08:8280901, Gm08:8280937, Gm08:8281564,Gm08:8282902, Gm08:8284027, Gm08:8286864, Gm08:8287265, Gm08:8287278,Gm08:8287453, Gm08:8287459, Gm08:8288039, Gm08:8288141, Gm08:8288200,Gm08:8288470, Gm08:8288831, Gm08:8289392, Gm08:8290740, Gm08:8291682,Gm08:8292207, Gm08:8297064, Gm08:8299433, Gm08:8299672, Gm08:8301839,Gm08:8302134, Gm08:8303450, Gm08:8305237, Gm08:8305348, Gm08:8305905,Gm08:8306090, Gm08:8306141, Gm08:8306210, Gm08:8306492, Gm08:8306627,Gm08:8307172, Gm08:8307665, Gm08:8308019, Gm08:8308891, Gm08:8308917,Gm08:8309316, Gm08:8309423, Gm08:8309837, Gm08:8310383, Gm08:8310464,Gm08:8310503, Gm08:8310663, Gm08:8311631, Gm08:8311906, Gm08:8312536,Gm08:8312819, Gm08:8313273, Gm08:8313923, Gm08:8314010, Gm08:8314025,Gm08:8314208, Gm08:8314292, Gm08:8314295, Gm08:8314513, Gm08:8314736,Gm08:8314791, Gm08:8314860, Gm08:8315543, Gm08:8315644, Gm08:8316113,Gm08:8316689, Gm08:8316899, Gm08:8317852, Gm08:8317861, Gm08:8318033,Gm08:8319087, Gm08:8319642, Gm08:8319647, Gm08:8320068, Gm08:8321253,Gm08:8321649, Gm08:8323937, Gm08:8324341, Gm08:8325127, Gm08:8325214,Gm08:8326696, Gm08:8326877, Gm08:8328633, Gm08:8330929, Gm08:8331132,Gm08:8331181, Gm08:8331408, Gm08:8331827, Gm08:8332651, Gm08:8332685,Gm08:8332957, Gm08:8343167, Gm08:8345187, Gm08:8345720, Gm08:8346030,Gm08:8346050, Gm08:8346352, Gm08:8346726, Gm08:8347799, Gm08:8348022,Gm08:8348028, Gm08:8349925, Gm08:8350122, Gm08:8350277, Gm08:8351061,Gm08:8351503, Gm08:8352313, Gm08:8352743, Gm08:8353341, Gm08:8355175,Gm08:8360133, Gm08:8363193, Gm08:8363888, Gm08:8364195 or a markerclosely linked thereto.2. The method of embodiment 1, wherein at least two marker loci aredetected.3. The method of embodiment 2, wherein the at least two marker locicomprise a haplotype that is associated with said resistance.4. The method of embodiment 1, wherein the germplasm is a soybeanvariety.5. The method of embodiment 1, wherein the method further comprisesselecting the first soybean plant or first soybean germplasm or aprogeny thereof having the at least one marker locus.6. The method of embodiment 5, further comprising crossing the selectedfirst soybean plant or first soybean germplasm with a second soybeanplant or second soybean germplasm.7. The method of embodiment 6, wherein the second soybean plant orsecond soybean germplasm comprises an exotic soybean strain or an elitesoybean strain.8. The method of embodiment 1, wherein the detecting comprises DNAsequencing of at least one of said marker loci.9. The method of embodiment 1, wherein the detecting comprisesamplifying at least one of said marker loci and detecting the resultingamplified marker amplicon.10. The method of embodiment 9, wherein the amplifying comprises:(a) admixing an amplification primer or amplification primer pair foreach marker locus being amplified with a nucleic acid isolated from thefirst soybean plant or the first soybean germplasm, wherein the primeror primer pair is complementary or partially complementary to a variantor fragment of the genomic locus comprising the marker locus, and iscapable of initiating DNA polymerization by a DNA polymerase using thesoybean nucleic acid as a template; and (b) extending the primer orprimer pair in a DNA polymerization reaction comprising a DNA polymeraseand a template nucleic acid to generate at least one amplicon.11. The method of embodiment 10, wherein said method comprisesamplifying a variant or fragment of one or more polynucleotidescomprising SEQ ID NOs: 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42,43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60,61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96,97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111,112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125,126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139,140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153,154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167,168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181,182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195,196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209,210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223,224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237,238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251,252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265,266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279,280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293,294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307,308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321,322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335,336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349,350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363,364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377,378, 379 or 380.12. The method of embodiment 10, wherein said primer or primer paircomprises a variant or fragment of one or more polynucleotidescomprising SEQ ID NOs: 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42,43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60,61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96,97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111,112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125,126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139,140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153,154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167,168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181,182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195,196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209,210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223,224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237,238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251,252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265,266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279,280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293,294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307,308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321,322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335,336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349,350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363,364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377,378, 379, 380 or complements thereof.13. The method of embodiment 12, wherein said primer or primer paircomprises a nucleic acid sequence comprising SEQ ID NOs: 1, 2, 3, 4, 5,6, 7, 8 or variants or fragments thereof.14. The method of embodiment 13, wherein said primer pair comprises SEQID NO: 1 and SEQ ID NO: 2.15. The method of embodiment 10, wherein the method further comprisesproviding one or more labeled nucleic acid probes suitable for detectionof each marker locus being amplified.16. The method of embodiment 15, wherein said labeled nucleic acid probecomprises a nucleic acid sequence comprising a variant or fragment ofone or more polynucleotides comprising SEQ ID NOs: 13, 14, 15, 16, 17,18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53,54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71,72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89,90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105,106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119,120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133,134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147,148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161,162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175,176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189,190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203,204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217,218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231,232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245,246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259,260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273,274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287,288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301,302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315,316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329,330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343,344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357,358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371,372, 373, 374, 375, 376, 377, 378, 379, 380 or complements thereof.17. The method of embodiment 16, wherein the labeled nucleic acid probecomprises a nucleic acid sequence comprising SEQ ID NOs: 9 or 10.18. An isolated polynucleotide capable of detecting a marker locus ofthe soybean genome comprising (a) S07160-1 or a marker closely linkedthereto on linkage group A2; or (b) Gm08:8300131, Gm08:8257778,Gm08:8257785, Gm08:8258163, Gm08:8258688, Gm08:8258742, Gm08:8259928,Gm08:8260451, Gm08:8260590, Gm08:8261480, Gm08:8261684, Gm08:8262165,Gm08:8263213, Gm08:8263250, Gm08:8263611, Gm08:8264149, Gm08:8265227,Gm08:8265364, Gm08:8265614, Gm08:8266183, Gm08:8266185, Gm08:8266263,Gm08:8266350, Gm08:8266386, Gm08:8266473, Gm08:8266888, Gm08:8267085,Gm08:8267166, Gm08:8267721, Gm08:8267826, Gm08:8268336, Gm08:8268861,Gm08:8269148, Gm08:8269785, Gm08:8270037, Gm08:8270562, Gm08:8270652,Gm08:8271540, Gm08:8271591, Gm08:8271649, Gm08:8271672, Gm08:8271955,Gm08:8273257, Gm08:8273355, Gm08:8273979, Gm08:8275766, Gm08:8275780,Gm08:8275959, Gm08:8276701, Gm08:8276849, Gm08:8276913, Gm08:8277162,Gm08:8277227, Gm08:8277248, Gm08:8277381, Gm08:8277383, Gm08:8277542,Gm08:8277625, Gm08:8277643, Gm08:8277876, Gm08:8277880, Gm08:8277969,Gm08:8278001, Gm08:8278167, Gm08:8278274, Gm08:8278434, Gm08:8279165,Gm08:8279230, Gm08:8279854, Gm08:8280901, Gm08:8280937, Gm08:8281564,Gm08:8282902, Gm08:8284027, Gm08:8286864, Gm08:8287265, Gm08:8287278,Gm08:8287453, Gm08:8287459, Gm08:8288039, Gm08:8288141, Gm08:8288200,Gm08:8288470, Gm08:8288831, Gm08:8289392, Gm08:8290740, Gm08:8291682,Gm08:8292207, Gm08:8297064, Gm08:8299433, Gm08:8299672, Gm08:8301839,Gm08:8302134, Gm08:8303450, Gm08:8305237, Gm08:8305348, Gm08:8305905,Gm08:8306090, Gm08:8306141, Gm08:8306210, Gm08:8306492, Gm08:8306627,Gm08:8307172, Gm08:8307665, Gm08:8308019, Gm08:8308891, Gm08:8308917,Gm08:8309316, Gm08:8309423, Gm08:8309837, Gm08:8310383, Gm08:8310464,Gm08:8310503, Gm08:8310663, Gm08:8311631, Gm08:8311906, Gm08:8312536,Gm08:8312819, Gm08:8313273, Gm08:8313923, Gm08:8314010, Gm08:8314025,Gm08:8314208, Gm08:8314292, Gm08:8314295, Gm08:8314513, Gm08:8314736,Gm08:8314791, Gm08:8314860, Gm08:8315543, Gm08:8315644, Gm08:8316113,Gm08:8316689, Gm08:8316899, Gm08:8317852, Gm08:8317861, Gm08:8318033,Gm08:8319087, Gm08:8319642, Gm08:8319647, Gm08:8320068, Gm08:8321253,Gm08:8321649, Gm08:8323937, Gm08:8324341, Gm08:8325127, Gm08:8325214,Gm08:8326696, Gm08:8326877, Gm08:8328633, Gm08:8330929, Gm08:8331132,Gm08:8331181, Gm08:8331408, Gm08:8331827, Gm08:8332651, Gm08:8332685,Gm08:8332957, Gm08:8343167, Gm08:8345187, Gm08:8345720, Gm08:8346030,Gm08:8346050, Gm08:8346352, Gm08:8346726, Gm08:8347799, Gm08:8348022,Gm08:8348028, Gm08:8349925, Gm08:8350122, Gm08:8350277, Gm08:8351061,Gm08:8351503, Gm08:8352313, Gm08:8352743, Gm08:8353341, Gm08:8355175,Gm08:8360133, Gm08:8363193, Gm08:8363888, Gm08:8364195 or a markerclosely linked thereto.19. The isolated polynucleotide of embodiment 18, wherein thepolynucleotide comprises: (a) a polynucleotide comprising SEQ ID NOs: 1,2, 3, 4, 5, 6, 7, or 8; (b) a polynucleotide comprising SEQ ID NOs: 9 or10; (c) a polynucleotide having at least 90% sequence identity to thepolynucleotides set forth in parts (a) or (b); or (d) a polynucleotidecomprising at least 10 contiguous nucleotides of the polynucleotides setforth in parts (a) or (b).20. A kit for detecting or selecting at least one soybean plant orsoybean germplasm with resistance or improved resistance to soybean cystnematode, the kit comprising:a) primers or probes for detecting one or more marker loci associatedwith resistance to soybean cyst nematode, wherein the primers or probesare capable of detecting a marker locus comprising (i) S07160-1 or amarker closely linked thereto; or (ii) Gm08:8300131, Gm08:8257778,Gm08:8257785, Gm08:8258163, Gm08:8258688, Gm08:8258742, Gm08:8259928,Gm08:8260451, Gm08:8260590, Gm08:8261480, Gm08:8261684, Gm08:8262165,Gm08:8263213, Gm08:8263250, Gm08:8263611, Gm08:8264149, Gm08:8265227,Gm08:8265364, Gm08:8265614, Gm08:8266183, Gm08:8266185, Gm08:8266263,Gm08:8266350, Gm08:8266386, Gm08:8266473, Gm08:8266888, Gm08:8267085,Gm08:8267166, Gm08:8267721, Gm08:8267826, Gm08:8268336, Gm08:8268861,Gm08:8269148, Gm08:8269785, Gm08:8270037, Gm08:8270562, Gm08:8270652,Gm08:8271540, Gm08:8271591, Gm08:8271649, Gm08:8271672, Gm08:8271955,Gm08:8273257, Gm08:8273355, Gm08:8273979, Gm08:8275766, Gm08:8275780,Gm08:8275959, Gm08:8276701, Gm08:8276849, Gm08:8276913, Gm08:8277162,Gm08:8277227, Gm08:8277248, Gm08:8277381, Gm08:8277383, Gm08:8277542,Gm08:8277625, Gm08:8277643, Gm08:8277876, Gm08:8277880, Gm08:8277969,Gm08:8278001, Gm08:8278167, Gm08:8278274, Gm08:8278434, Gm08:8279165,Gm08:8279230, Gm08:8279854, Gm08:8280901, Gm08:8280937, Gm08:8281564,Gm08:8282902, Gm08:8284027, Gm08:8286864, Gm08:8287265, Gm08:8287278,Gm08:8287453, Gm08:8287459, Gm08:8288039, Gm08:8288141, Gm08:8288200,Gm08:8288470, Gm08:8288831, Gm08:8289392, Gm08:8290740, Gm08:8291682,Gm08:8292207, Gm08:8297064, Gm08:8299433, Gm08:8299672, Gm08:8301839,Gm08:8302134, Gm08:8303450, Gm08:8305237, Gm08:8305348, Gm08:8305905,Gm08:8306090, Gm08:8306141, Gm08:8306210, Gm08:8306492, Gm08:8306627,Gm08:8307172, Gm08:8307665, Gm08:8308019, Gm08:8308891, Gm08:8308917,Gm08:8309316, Gm08:8309423, Gm08:8309837, Gm08:8310383, Gm08:8310464,Gm08:8310503, Gm08:8310663, Gm08:8311631, Gm08:8311906, Gm08:8312536,Gm08:8312819, Gm08:8313273, Gm08:8313923, Gm08:8314010, Gm08:8314025,Gm08:8314208, Gm08:8314292, Gm08:8314295, Gm08:8314513, Gm08:8314736,Gm08:8314791, Gm08:8314860, Gm08:8315543, Gm08:8315644, Gm08:8316113,Gm08:8316689, Gm08:8316899, Gm08:8317852, Gm08:8317861, Gm08:8318033,Gm08:8319087, Gm08:8319642, Gm08:8319647, Gm08:8320068, Gm08:8321253,Gm08:8321649, Gm08:8323937, Gm08:8324341, Gm08:8325127, Gm08:8325214,Gm08:8326696, Gm08:8326877, Gm08:8328633, Gm08:8330929, Gm08:8331132,Gm08:8331181, Gm08:8331408, Gm08:8331827, Gm08:8332651, Gm08:8332685,Gm08:8332957, Gm08:8343167, Gm08:8345187, Gm08:8345720, Gm08:8346030,Gm08:8346050, Gm08:8346352, Gm08:8346726, Gm08:8347799, Gm08:8348022,Gm08:8348028, Gm08:8349925, Gm08:8350122, Gm08:8350277, Gm08:8351061,Gm08:8351503, Gm08:8352313, Gm08:8352743, Gm08:8353341, Gm08:8355175,Gm08:8360133, Gm08:8363193, Gm08:8363888, Gm08:8364195 or a markerclosely linked thereto; and b) instructions for using the primers orprobes for detecting the one or more marker loci and correlating thedetected marker loci with predicted resistance to soybean cyst nematode.

EXPERIMENTAL

The following examples are offered to illustrate, but not to limit theclaimed invention. It is understood that the examples and embodimentsdescribed herein are for illustrative purposes only, and persons skilledin the art will recognize various reagents or parameters that can bealtered without departing from the spirit of the invention or the scopeof the appended claims.

Example 1 Marker Loci Associated with Soybean Cyst Nematode Resistanceon Linkage Group A2

A SNP marker for the Rhg4 locus (Soybean Cyst Nematode Resistance) onLinkage Group A2 was developed for use in high throughput genotypescreening, this marker, as well as markers genetically associated tothis marker, are provided. Markers from this region are relevant toelite breeding populations and facilitate selection of soybean plantswith resistance to SCN at the Rhg4 locus tracing back to PI437654 andPeking as well as stacks with other marker assisted traits, includingyield genes.

S07160-1-Q1 was developed and optimized for high throughput PCR-basedmethods, such as Taqman™ assays. Optimization involved evaluation ofamplification, Res, Sus, and heterozygous clustering, primer length,primer composition and the like. The marker distinguishes between theresistant allele from P1437654 or Peking (C) and a susceptible allelefrom BSR101 (A). Primers and probes useful for detecting thepolymorphism are summarized below in Tables 6 and 7, respectively.

TABLE 6  Primers Oligo Product Primers: ID Sequence Size Primer 1 136868TGTGTTGTGTTTGACTGCCATA (SEQ ID NO: 1) Primer 2 136869CATTTCCCAAGCCTCTTGAT 117 bp (SEQ ID NO: 2)

TABLE 7  Probes Probes: Sequence 1023896FAM-ACTAACTGCATAaGATAT (SEQ ID NO: 9) 102390VIC-CTAACTGCATAcGATATT (SEQ ID NO: 10)

The marker was validated against a panel of 31 public or proprietarysoybean lines comprising 2 resistant check lines, 27 susceptible lines,and 2 other lines. A summary of the rhg4 marker is provided below inTable 8.

Exemplary Amplification Mix H20 4.28 ul Hot Tub buffer 0.5 ul Rox Dye(50X) 0.075 ul DNTPs(24 mM each) 0.039 ul Primer(100 uM) 0.0375 ulPrimer(100 uM) 0.0375 ul FAM Probe(100 uM 0.005 ul VIC Probe(100 uM0.005 ul Hot Tub enzyme 0.025 ul Total volume 5.005 ul

TABLE 8 Summary of rhg4 marker. Genetic Position Physical Pos_PHI Gene/(genetic map); Map Allele Public Consensus locus Markers LG GmConsensus4.0 Position (R/S) Source Name Map v1.1 rhg4 S07160-1 A2 46.68 8300131C/A Peking, pBLT65 51.42 PI437654 R = Resistant; S = Susceptible

Example 2 Identification of SNPs in Linkage Disequilibrium with KnownMutations at the Rhg4 Locus SUMMARY

The Rhg4 locus, which conditions resistance to soybean cyst nematode,has been cloned and found to encode a serine hydroxymethyltransferase(Liu et al. (2012). A soybean cyst nematode resistance gene points to anew mechanism of plant resistance to pathogens. Nature 492, 256-260).Two non-synonymous base substitutions that tightly correlate with SCNresistance were identified in the Rhg4 allele from the resistant sourceForrest (Liu et al. Nature, 2012). Using SNP genotype data obtained fromre-sequencing 385 Pioneer proprietary elite lines, 181 SNPs wereidentified that are in high linkage disequilibrium with the describedmutations. These SNPs can be used for a variety of plant breedingefforts, including marker assisted selection of the Rhg4 locus.

Methods:

Linkage Disequilibrium was calculated using Haploview 4.2. 7810 SNP lociwere evaluated across 385 elite lines. An interval of ˜1.2 mb or 6.5 cM(Gm08:7800225-8999989 bp; 48.26-54.80 cM) spanning the Rhg4 mutationswas interrogated for SNP selection. An r² above or equal to 0.8 isconsidered high for this analysis. Haploview settings were set asfollows: Ignore Pairwise comparisons: >100 kb; HW p-value cutoff: 0.000;Min genotype %: 50; Max # mendel errors: 1; Min Minor AlleleFrequency=0.01.

Results

The 181 Rhg4 SNPs in Linkage Disequilibrium with the described mutations(Liu et al. Nature, 2012) are summarized in Table 3B.

TABLE 9 Summary of SEQ ID NOs. SEQ ID NO Description 1 Primer 136868 2Primer 136869 3 Primer 100532 4 Primer 80588 5 Primer 136870 6 Primer136871 7 Primer 136872 8 Primer 136873 9 Probe 102389 10 Probe 102390 11Amplicon comprising resistance allele 12 Amplicon comprising susceptibleallele 13 Reference Sequence comprising S07160-1 resistance allele 14Reference Sequence comprising S07160-1 susceptible allele 15-380Consensus Reference Sequences comprising the various marker lociprovided herein (see Table 3B)

All publications and patent applications mentioned in the specificationare indicative of the level of those skilled in the art to which thisinvention pertains. All publications and patent applications are hereinincorporated by reference to the same extent as if each individualpublication or patent application was specifically and individuallyindicated to be incorporated by reference.

Although the foregoing invention has been described in some detail byway of illustration and example for purposes of clarity ofunderstanding, it will be obvious that certain changes and modificationsmay be practiced within the scope of the appended claims.

That which is claimed:
 1. A method of identifying a first soybean plantor a first soybean germplasm that displays resistance or improvedresistance to soybean cyst nematode, the method comprising detecting inthe genome of said first soybean plant or in the genome of said firstsoybean germplasm at least one marker locus that is associated with theresistance, wherein the at least one marker locus comprises (a) S07160-1or a marker closely linked thereto on linkage group A2; or (b)Gm08:8300131, Gm08:8257778, Gm08:8257785, Gm08:8258163, Gm08:8258688,Gm08:8258742, Gm08:8259928, Gm08:8260451, Gm08:8260590, Gm08:8261480,Gm08:8261684, Gm08:8262165, Gm08:8263213, Gm08:8263250, Gm08:8263611,Gm08:8264149, Gm08:8265227, Gm08:8265364, Gm08:8265614, Gm08:8266183,Gm08:8266185, Gm08:8266263, Gm08:8266350, Gm08:8266386, Gm08:8266473,Gm08:8266888, Gm08:8267085, Gm08:8267166, Gm08:8267721, Gm08:8267826,Gm08:8268336, Gm08:8268861, Gm08:8269148, Gm08:8269785, Gm08:8270037,Gm08:8270562, Gm08:8270652, Gm08:8271540, Gm08:8271591, Gm08:8271649,Gm08:8271672, Gm08:8271955, Gm08:8273257, Gm08:8273355, Gm08:8273979,Gm08:8275766, Gm08:8275780, Gm08:8275959, Gm08:8276701, Gm08:8276849,Gm08:8276913, Gm08:8277162, Gm08:8277227, Gm08:8277248, Gm08:8277381,Gm08:8277383, Gm08:8277542, Gm08:8277625, Gm08:8277643, Gm08:8277876,Gm08:8277880, Gm08:8277969, Gm08:8278001, Gm08:8278167, Gm08:8278274,Gm08:8278434, Gm08:8279165, Gm08:8279230, Gm08:8279854, Gm08:8280901,Gm08:8280937, Gm08:8281564, Gm08:8282902, Gm08:8284027, Gm08:8286864,Gm08:8287265, Gm08:8287278, Gm08:8287453, Gm08:8287459, Gm08:8288039,Gm08:8288141, Gm08:8288200, Gm08:8288470, Gm08:8288831, Gm08:8289392,Gm08:8290740, Gm08:8291682, Gm08:8292207, Gm08:8297064, Gm08:8299433,Gm08:8299672, Gm08:8301839, Gm08:8302134, Gm08:8303450, Gm08:8305237,Gm08:8305348, Gm08:8305905, Gm08:8306090, Gm08:8306141, Gm08:8306210,Gm08:8306492, Gm08:8306627, Gm08:8307172, Gm08:8307665, Gm08:8308019,Gm08:8308891, Gm08:8308917, Gm08:8309316, Gm08:8309423, Gm08:8309837,Gm08:8310383, Gm08:8310464, Gm08:8310503, Gm08:8310663, Gm08:8311631,Gm08:8311906, Gm08:8312536, Gm08:8312819, Gm08:8313273, Gm08:8313923,Gm08:8314010, Gm08:8314025, Gm08:8314208, Gm08:8314292, Gm08:8314295,Gm08:8314513, Gm08:8314736, Gm08:8314791, Gm08:8314860, Gm08:8315543,Gm08:8315644, Gm08:8316113, Gm08:8316689, Gm08:8316899, Gm08:8317852,Gm08:8317861, Gm08:8318033, Gm08:8319087, Gm08:8319642, Gm08:8319647,Gm08:8320068, Gm08:8321253, Gm08:8321649, Gm08:8323937, Gm08:8324341,Gm08:8325127, Gm08:8325214, Gm08:8326696, Gm08:8326877, Gm08:8328633,Gm08:8330929, Gm08:8331132, Gm08:8331181, Gm08:8331408, Gm08:8331827,Gm08:8332651, Gm08:8332685, Gm08:8332957, Gm08:8343167, Gm08:8345187,Gm08:8345720, Gm08:8346030, Gm08:8346050, Gm08:8346352, Gm08:8346726,Gm08:8347799, Gm08:8348022, Gm08:8348028, Gm08:8349925, Gm08:8350122,Gm08:8350277, Gm08:8351061, Gm08:8351503, Gm08:8352313, Gm08:8352743,Gm08:8353341, Gm08:8355175, Gm08:8360133, Gm08:8363193, Gm08:8363888,Gm08:8364195 or a marker closely linked thereto.
 2. The method of claim1, wherein at least two marker loci are detected.
 3. The method of claim2, wherein the at least two marker loci comprise a haplotype that isassociated with said resistance.
 4. The method of claim 1, wherein thegermplasm is a soybean variety.
 5. The method of claim 1, wherein themethod further comprises selecting the first soybean plant or firstsoybean germplasm or a progeny thereof having the at least one markerlocus.
 6. The method of claim 5, further comprising crossing theselected first soybean plant or first soybean germplasm with a secondsoybean plant or second soybean germplasm.
 7. The method of claim 6,wherein the second soybean plant or second soybean germplasm comprisesan exotic soybean strain or an elite soybean strain.
 8. The method ofclaim 1, wherein the detecting comprises DNA sequencing of at least oneof said marker loci.
 9. The method of claim 1, wherein the detectingcomprises amplifying at least one of said marker loci and detecting theresulting amplified marker amplicon.
 10. The method of claim 9, whereinthe amplifying comprises: a) admixing an amplification primer oramplification primer pair for each marker locus being amplified with anucleic acid isolated from the first soybean plant or the first soybeangermplasm, wherein the primer or primer pair is complementary orpartially complementary to a variant or fragment of the genomic locuscomprising the marker locus, and is capable of initiating DNApolymerization by a DNA polymerase using the soybean nucleic acid as atemplate; and b) extending the primer or primer pair in a DNApolymerization reaction comprising a DNA polymerase and a templatenucleic acid to generate at least one amplicon.
 11. The method of claim10, wherein said method comprises amplifying a variant or fragment ofone or more polynucleotides comprising SEQ ID NOs: 13, 14, 15, 16, 17,18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53,54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71,72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89,90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105,106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119,120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133,134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147,148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161,162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175,176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189,190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203,204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217,218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231,232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245,246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259,260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273,274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287,288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301,302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315,316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329,330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343,344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357,358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371,372, 373, 374, 375, 376, 377, 378, 379 or
 380. 12. The method of claim10, wherein said primer or primer pair comprises a variant or fragmentof one or more polynucleotides comprising SEQ ID NOs: 13, 14, 15, 16,17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34,35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52,53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70,71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88,89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104,105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118,119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132,133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146,147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160,161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174,175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188,189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202,203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216,217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230,231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244,245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258,259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272,273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286,287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300,301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314,315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328,329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342,343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356,357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370,371, 372, 373, 374, 375, 376, 377, 378, 379, 380 or complements thereof.13. The method of claim 12, wherein said primer or primer pair comprisesa nucleic acid sequence comprising SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8 orvariants or fragments thereof.
 14. The method of claim 13, wherein saidprimer pair comprises SEQ ID NO: 1 and SEQ ID NO:
 2. 15. The method ofclaim 10, wherein the method further comprises providing one or morelabeled nucleic acid probes suitable for detection of each marker locusbeing amplified.
 16. The method of claim 15, wherein said labelednucleic acid probe comprises a nucleic acid sequence comprising avariant or fragment of one or more polynucleotides comprising SEQ IDNOs: 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29,30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65,66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83,84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100,101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114,115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128,129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142,143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156,157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170,171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184,185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198,199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212,213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226,227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240,241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254,255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268,269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282,283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296,297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310,311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324,325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338,339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352,353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366,367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380 orcomplements thereof.
 17. The method of claim 16, wherein the labelednucleic acid probe comprises a nucleic acid sequence comprising SEQ IDNOs: 9 or
 10. 18. An isolated polynucleotide capable of detecting amarker locus of the soybean genome comprising (a) S07160-1 or a markerclosely linked thereto on linkage group A2; or (b) Gm08:8300131,Gm08:8257778, Gm08:8257785, Gm08:8258163, Gm08:8258688, Gm08:8258742,Gm08:8259928, Gm08:8260451, Gm08:8260590, Gm08:8261480, Gm08:8261684,Gm08:8262165, Gm08:8263213, Gm08:8263250, Gm08:8263611, Gm08:8264149,Gm08:8265227, Gm08:8265364, Gm08:8265614, Gm08:8266183, Gm08:8266185,Gm08:8266263, Gm08:8266350, Gm08:8266386, Gm08:8266473, Gm08:8266888,Gm08:8267085, Gm08:8267166, Gm08:8267721, Gm08:8267826, Gm08:8268336,Gm08:8268861, Gm08:8269148, Gm08:8269785, Gm08:8270037, Gm08:8270562,Gm08:8270652, Gm08:8271540, Gm08:8271591, Gm08:8271649, Gm08:8271672,Gm08:8271955, Gm08:8273257, Gm08:8273355, Gm08:8273979, Gm08:8275766,Gm08:8275780, Gm08:8275959, Gm08:8276701, Gm08:8276849, Gm08:8276913,Gm08:8277162, Gm08:8277227, Gm08:8277248, Gm08:8277381, Gm08:8277383,Gm08:8277542, Gm08:8277625, Gm08:8277643, Gm08:8277876, Gm08:8277880,Gm08:8277969, Gm08:8278001, Gm08:8278167, Gm08:8278274, Gm08:8278434,Gm08:8279165, Gm08:8279230, Gm08:8279854, Gm08:8280901, Gm08:8280937,Gm08:8281564, Gm08:8282902, Gm08:8284027, Gm08:8286864, Gm08:8287265,Gm08:8287278, Gm08:8287453, Gm08:8287459, Gm08:8288039, Gm08:8288141,Gm08:8288200, Gm08:8288470, Gm08:8288831, Gm08:8289392, Gm08:8290740,Gm08:8291682, Gm08:8292207, Gm08:8297064, Gm08:8299433, Gm08:8299672,Gm08:8301839, Gm08:8302134, Gm08:8303450, Gm08:8305237, Gm08:8305348,Gm08:8305905, Gm08:8306090, Gm08:8306141, Gm08:8306210, Gm08:8306492,Gm08:8306627, Gm08:8307172, Gm08:8307665, Gm08:8308019, Gm08:8308891,Gm08:8308917, Gm08:8309316, Gm08:8309423, Gm08:8309837, Gm08:8310383,Gm08:8310464, Gm08:8310503, Gm08:8310663, Gm08:8311631, Gm08:8311906,Gm08:8312536, Gm08:8312819, Gm08:8313273, Gm08:8313923, Gm08:8314010,Gm08:8314025, Gm08:8314208, Gm08:8314292, Gm08:8314295, Gm08:8314513,Gm08:8314736, Gm08:8314791, Gm08:8314860, Gm08:8315543, Gm08:8315644,Gm08:8316113, Gm08:8316689, Gm08:8316899, Gm08:8317852, Gm08:8317861,Gm08:8318033, Gm08:8319087, Gm08:8319642, Gm08:8319647, Gm08:8320068,Gm08:8321253, Gm08:8321649, Gm08:8323937, Gm08:8324341, Gm08:8325127,Gm08:8325214, Gm08:8326696, Gm08:8326877, Gm08:8328633, Gm08:8330929,Gm08:8331132, Gm08:8331181, Gm08:8331408, Gm08:8331827, Gm08:8332651,Gm08:8332685, Gm08:8332957, Gm08:8343167, Gm08:8345187, Gm08:8345720,Gm08:8346030, Gm08:8346050, Gm08:8346352, Gm08:8346726, Gm08:8347799,Gm08:8348022, Gm08:8348028, Gm08:8349925, Gm08:8350122, Gm08:8350277,Gm08:8351061, Gm08:8351503, Gm08:8352313, Gm08:8352743, Gm08:8353341,Gm08:8355175, Gm08:8360133, Gm08:8363193, Gm08:8363888, Gm08:8364195 ora marker closely linked thereto.
 19. The isolated polynucleotide ofclaim 18, wherein the polynucleotide comprises: (a) a polynucleotidecomprising SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, or 8; (b) a polynucleotidecomprising SEQ ID NOs: 9 or 10; (c) a polynucleotide having at least 90%sequence identity to the polynucleotides set forth in parts (a) or (b);or (d) a polynucleotide comprising at least 10 contiguous nucleotides ofthe polynucleotides set forth in parts (a) or (b).
 20. A kit fordetecting or selecting at least one soybean plant or soybean germplasmwith resistance or improved resistance to soybean cyst nematode, the kitcomprising: a) primers or probes for detecting one or more marker lociassociated with resistance to soybean cyst nematode, wherein the primersor probes are capable of detecting a marker locus comprising (i)S07160-1 or a marker closely linked thereto; or (ii) Gm08:8300131,Gm08:8257778, Gm08:8257785, Gm08:8258163, Gm08:8258688, Gm08:8258742,Gm08:8259928, Gm08:8260451, Gm08:8260590, Gm08:8261480, Gm08:8261684,Gm08:8262165, Gm08:8263213, Gm08:8263250, Gm08:8263611, Gm08:8264149,Gm08:8265227, Gm08:8265364, Gm08:8265614, Gm08:8266183, Gm08:8266185,Gm08:8266263, Gm08:8266350, Gm08:8266386, Gm08:8266473, Gm08:8266888,Gm08:8267085, Gm08:8267166, Gm08:8267721, Gm08:8267826, Gm08:8268336,Gm08:8268861, Gm08:8269148, Gm08:8269785, Gm08:8270037, Gm08:8270562,Gm08:8270652, Gm08:8271540, Gm08:8271591, Gm08:8271649, Gm08:8271672,Gm08:8271955, Gm08:8273257, Gm08:8273355, Gm08:8273979, Gm08:8275766,Gm08:8275780, Gm08:8275959, Gm08:8276701, Gm08:8276849, Gm08:8276913,Gm08:8277162, Gm08:8277227, Gm08:8277248, Gm08:8277381, Gm08:8277383,Gm08:8277542, Gm08:8277625, Gm08:8277643, Gm08:8277876, Gm08:8277880,Gm08:8277969, Gm08:8278001, Gm08:8278167, Gm08:8278274, Gm08:8278434,Gm08:8279165, Gm08:8279230, Gm08:8279854, Gm08:8280901, Gm08:8280937,Gm08:8281564, Gm08:8282902, Gm08:8284027, Gm08:8286864, Gm08:8287265,Gm08:8287278, Gm08:8287453, Gm08:8287459, Gm08:8288039, Gm08:8288141,Gm08:8288200, Gm08:8288470, Gm08:8288831, Gm08:8289392, Gm08:8290740,Gm08:8291682, Gm08:8292207, Gm08:8297064, Gm08:8299433, Gm08:8299672,Gm08:8301839, Gm08:8302134, Gm08:8303450, Gm08:8305237, Gm08:8305348,Gm08:8305905, Gm08:8306090, Gm08:8306141, Gm08:8306210, Gm08:8306492,Gm08:8306627, Gm08:8307172, Gm08:8307665, Gm08:8308019, Gm08:8308891,Gm08:8308917, Gm08:8309316, Gm08:8309423, Gm08:8309837, Gm08:8310383,Gm08:8310464, Gm08:8310503, Gm08:8310663, Gm08:8311631, Gm08:8311906,Gm08:8312536, Gm08:8312819, Gm08:8313273, Gm08:8313923, Gm08:8314010,Gm08:8314025, Gm08:8314208, Gm08:8314292, Gm08:8314295, Gm08:8314513,Gm08:8314736, Gm08:8314791, Gm08:8314860, Gm08:8315543, Gm08:8315644,Gm08:8316113, Gm08:8316689, Gm08:8316899, Gm08:8317852, Gm08:8317861,Gm08:8318033, Gm08:8319087, Gm08:8319642, Gm08:8319647, Gm08:8320068,Gm08:8321253, Gm08:8321649, Gm08:8323937, Gm08:8324341, Gm08:8325127,Gm08:8325214, Gm08:8326696, Gm08:8326877, Gm08:8328633, Gm08:8330929,Gm08:8331132, Gm08:8331181, Gm08:8331408, Gm08:8331827, Gm08:8332651,Gm08:8332685, Gm08:8332957, Gm08:8343167, Gm08:8345187, Gm08:8345720,Gm08:8346030, Gm08:8346050, Gm08:8346352, Gm08:8346726, Gm08:8347799,Gm08:8348022, Gm08:8348028, Gm08:8349925, Gm08:8350122, Gm08:8350277,Gm08:8351061, Gm08:8351503, Gm08:8352313, Gm08:8352743, Gm08:8353341,Gm08:8355175, Gm08:8360133, Gm08:8363193, Gm08:8363888, Gm08:8364195 ora marker closely linked thereto; and b) instructions for using theprimers or probes for detecting the one or more marker loci andcorrelating the detected marker loci with predicted resistance tosoybean cyst nematode.